OK, so the current problem seems to be that I cannot get the ntlm_auth to work. 
I read 
http://freeradius.1045715.n5.nabble.com/Freeradius-with-Active-Directory-td2747221.html
 but that does not seem to apply for me as the ntlm_auth file contains the 
exec. 

Attached (if that works) is the radius -X output for the current working 
configuration (basic_configuration_run.txt). We are only doing 
mac-authentication now and depending on the mac-address, the device is placed 
in a certain VLAN. I unfortunately did not install the server myself but as far 
as I know FR was originally installed from the Debian package 2.1.8 and we 
recently upgraded to 2.1.10.

Until a year ago I never really worked with (free)radius, linux or cisco 
switches and it still is just a small part of my daily work, so I probably make 
a lot of beginner mistakes.

# -*- text -*-
#
#  $Id$
# NTLM module
#
#  To authenticate requests using AD.
#
exec ntlm_auth {
        wait = yes
        program = "/usr/bin/ntlm_auth --request-nt-key --domain=ALEO.LOCAL 
--username=%{mschap:User-Name} --password=%{User-Password}"
}

If I add ntlm_auth to the beginning of the users file I get an error
/etc/freeradius/users[157]: Parse error (check) for entry DEFAULT: Unknown 
value ntlm_auth for attribute Auth-Type
Errors reading /etc/freeradius/users

If I add ntlm_auth to the authenticate section of the default virtual server I 
get an error
/etc/freeradius/sites-enabled/default[254]: Failed to load module "ntlm_auth".
/etc/freeradius/sites-enabled/default[217]: Errors parsing authenticate section.

If I add ntlm_auth to the modules section of radiusd.conf I get a 'warning'
/etc/freeradius/radiusd.conf[1840]: Failed to link to module 'rlm_ntlm_auth': 
file not found
FreeRADIUS Version 2.1.10, for host x86_64-pc-linux-gnu, built on Nov 14 2010 
at 21:14:10
Copyright (C) 1999-2009 The FreeRADIUS server project and contributors. 
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A 
PARTICULAR PURPOSE. 
You may redistribute copies of FreeRADIUS under the terms of the 
GNU General Public License v2. 
Starting - reading configuration files ...
including configuration file /etc/freeradius/radiusd.conf
including configuration file /etc/freeradius/proxy.conf
including configuration file /etc/freeradius/clients.conf
including configuration file /etc/freeradius/modules/files
including configuration file /etc/freeradius/eap.conf
including configuration file /etc/freeradius/policy.conf
including files in directory /etc/freeradius/sites-enabled/
including configuration file /etc/freeradius/sites-enabled/inner-tunnel
including configuration file /etc/freeradius/sites-enabled/default
main {
        user = "freerad"
        group = "freerad"
        allow_core_dumps = no
}
including dictionary file /etc/freeradius/dictionary
main {
        prefix = "/usr"
        localstatedir = "/var"
        logdir = "/var/log/freeradius"
        libdir = "/usr/lib/freeradius"
        radacctdir = "/var/log/freeradius/radacct"
        hostname_lookups = no
        max_request_time = 30
        cleanup_delay = 5
        max_requests = 1024
        pidfile = "/var/run/freeradius/freeradius.pid"
        checkrad = "/usr/sbin/checkrad"
        debug_level = 0
        proxy_requests = yes
 log {
        stripped_names = no
        auth = no
        auth_badpass = no
        auth_goodpass = no
 }
 security {
        max_attributes = 200
        reject_delay = 1
        status_server = yes
 }
}
radiusd: #### Loading Realms and Home Servers ####
 proxy server {
        retry_delay = 5
        retry_count = 3
        default_fallback = no
        dead_time = 120
        wake_all_if_all_dead = no
 }
 home_server localhost {
        ipaddr = 127.0.0.1
        port = 1812
        type = "auth"
        secret = "testing123"
        response_window = 20
        max_outstanding = 65536
        require_message_authenticator = yes
        zombie_period = 40
        status_check = "status-server"
        ping_interval = 30
        check_interval = 30
        num_answers_to_alive = 3
        num_pings_to_alive = 3
        revive_interval = 120
        status_check_timeout = 4
        irt = 2
        mrt = 16
        mrc = 5
        mrd = 30
 }
 home_server_pool my_auth_failover {
        type = fail-over
        home_server = localhost
 }
 realm example.com {
        auth_pool = my_auth_failover
 }
 realm LOCAL {
 }
radiusd: #### Loading Clients ####
 client localhost {
        ipaddr = 127.0.0.1
        require_message_authenticator = no
        secret = "secret"
        nastype = "other"
 }
 client 10.1.1.201 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.201"
        nastype = "cisco"
 }
 client 10.1.1.202 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.202"
        nastype = "cisco"
 }
 client 10.1.1.203 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.203"
        nastype = "cisco"
 }
 client 10.1.1.204 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.204"
        nastype = "cisco"
 }
 client 10.1.1.205 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.205"
        nastype = "cisco"
 }
 client 10.1.1.206 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.206"
        nastype = "cisco"
 }
 client 10.1.1.207 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.207"
        nastype = "cisco"
 }
 client 10.1.1.208 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.208"
        nastype = "cisco"
 }
 client 10.1.1.209 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.209"
        nastype = "cisco"
 }
 client 10.1.1.210 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "10.1.1.210"
        nastype = "cisco"
 }
 client 10.1.1.42 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "wlc"
        nastype = "cisco"
 }
 client 10.1.2.0/24 {
        require_message_authenticator = no
        secret = "secret"
        shortname = "network"
 }
radiusd: #### Instantiating modules ####
 instantiate {
 Module: Linked to module rlm_exec
 Module: Instantiating module "exec" from file /etc/freeradius/radiusd.conf
  exec {
        wait = yes
        input_pairs = "request"
        shell_escape = yes
  }
 Module: Linked to module rlm_expr
 Module: Instantiating module "expr" from file /etc/freeradius/radiusd.conf
 Module: Linked to module rlm_expiration
 Module: Instantiating module "expiration" from file 
/etc/freeradius/radiusd.conf
  expiration {
        reply-message = "Password Has Expired  "
  }
 Module: Linked to module rlm_logintime
 Module: Instantiating module "logintime" from file /etc/freeradius/radiusd.conf
  logintime {
        reply-message = "You are calling outside your allowed timespan  "
        minimum-timeout = 60
  }
 }
radiusd: #### Loading Virtual Servers ####
server { # from file /etc/freeradius/radiusd.conf
 modules {
 Module: Checking authenticate {...} for more modules to load
 Module: Linked to module rlm_pap
 Module: Instantiating module "pap" from file /etc/freeradius/radiusd.conf
  pap {
        encryption_scheme = "auto"
        auto_header = no
  }
 Module: Linked to module rlm_eap
 Module: Instantiating module "eap" from file /etc/freeradius/eap.conf
  eap {
        default_eap_type = "md5"
        timer_expire = 60
        ignore_unknown_eap_types = no
        cisco_accounting_username_bug = no
        max_sessions = 4096
  }
 Module: Linked to sub-module rlm_eap_md5
 Module: Instantiating eap-md5
 Module: Linked to sub-module rlm_eap_leap
 Module: Instantiating eap-leap
 Module: Linked to sub-module rlm_eap_gtc
 Module: Instantiating eap-gtc
   gtc {
        challenge = "Password: "
        auth_type = "PAP"
   }
 Module: Linked to module rlm_chap
 Module: Instantiating module "chap" from file /etc/freeradius/radiusd.conf
 Module: Linked to module rlm_always
 Module: Instantiating module "ok" from file /etc/freeradius/radiusd.conf
  always ok {
        rcode = "ok"
        simulcount = 0
        mpp = no
  }
 Module: Checking authorize {...} for more modules to load
 Module: Linked to module rlm_detail
 Module: Instantiating module "auth_log" from file /etc/freeradius/radiusd.conf
  detail auth_log {
        detailfile = 
"/var/log/freeradius/radacct/%{Calling-Station-ID}/auth-detail-%Y%m%d"
        header = "%t"
        detailperm = 384
        dirperm = 493
        locking = no
        log_packet_header = no
  }
 Module: Linked to module rlm_files
 Module: Instantiating module "files" from file /etc/freeradius/radiusd.conf
  files {
        usersfile = "/etc/freeradius/users"
        acctusersfile = "/etc/freeradius/acct_users"
        preproxy_usersfile = "/etc/freeradius/preproxy_users"
        compat = "no"
  }
 Module: Checking accounting {...} for more modules to load
 Module: Instantiating module "detail" from file /etc/freeradius/radiusd.conf
  detail {
        detailfile = 
"/var/log/freeradius/radacct/%{Calling-Station-ID}/detail-%Y%m%d"
        header = "%t"
        detailperm = 384
        dirperm = 493
        locking = no
        log_packet_header = no
  }
 Module: Linked to module rlm_radutmp
 Module: Instantiating module "radutmp" from file /etc/freeradius/radiusd.conf
  radutmp {
        filename = "/var/log/freeradius/radutmp"
        username = "%{User-Name}"
        case_sensitive = no
        check_with_nas = yes
        perm = 384
        callerid = yes
  }
 Module: Checking session {...} for more modules to load
 Module: Checking post-auth {...} for more modules to load
 Module: Instantiating module "reply_log" from file /etc/freeradius/radiusd.conf
  detail reply_log {
        detailfile = 
"/var/log/freeradius/radacct/%{Calling-Station-ID}/reply-detail-%Y%m%d"
        header = "%t"
        detailperm = 384
        dirperm = 493
        locking = no
        log_packet_header = no
  }
 Module: Instantiating module "authorized_phones" from file 
/etc/freeradius/modules/files
  files authorized_phones {
        usersfile = "/etc/freeradius/authorized_phones"
        compat = "no"
        key = "%{tolower:%{Calling-Station-ID}}"
  }
 Module: Instantiating module "authorized_atas" from file 
/etc/freeradius/modules/files
  files authorized_atas {
        usersfile = "/etc/freeradius/authorized_atas"
        compat = "no"
        key = "%{tolower:%{Calling-Station-ID}}"
  }
 Module: Instantiating module "authorized_printers" from file 
/etc/freeradius/modules/files
  files authorized_printers {
        usersfile = "/etc/freeradius/authorized_printers"
        compat = "no"
        key = "%{tolower:%{Calling-Station-ID}}"
  }
 Module: Instantiating module "authorized_test" from file 
/etc/freeradius/modules/files
  files authorized_test {
        usersfile = "/etc/freeradius/authorized_test"
        compat = "no"
        key = "%{tolower:%{Calling-Station-ID}}"
  }
 Module: Instantiating module "authorized_macs" from file 
/etc/freeradius/modules/files
  files authorized_macs {
        usersfile = "/etc/freeradius/authorized_macs"
        compat = "no"
        key = "%{tolower:%{Calling-Station-ID}}"
  }
 Module: Instantiating module "reject" from file /etc/freeradius/radiusd.conf
  always reject {
        rcode = "reject"
        simulcount = 0
        mpp = no
  }
 } # modules
} # server
radiusd: #### Opening IP addresses and Ports ####
listen {
        type = "auth"
        ipaddr = *
        port = 0
}
listen {
        type = "acct"
        ipaddr = *
        port = 0
}
Listening on authentication address * port 1812
Listening on accounting address * port 1813
Listening on proxy address * port 1814
Ready to process requests.
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