Looking at your command from your terminal example and then looking at your 
command_line from your Nagios definition and your check_command statement the 
fields all seems to be backwards

The things that I can see are

-          Your Nagios configuration is using the root account to connect to 
the server and your command line definition is using Nagios

-          Your command_line is being passwd 'ipxenserver' as the remote 
command to execute

-          You command_line is being passwd your remote command as the ssh key 
to use.

-          You have a trailing ! in your check_command definition which we 
create a variable with no value

I think your command definition and need to be updated, something like this

define command{
        command_name    check_xen_cpu
        command_line    $USER1$/check_by_ssh -l $ARG1$ H $HOSTADDRESS$ -C 
$ARG2$ -I $ARG3$
        }

define service {
       service_description                 XenServer CPU Load
       host_name                                  ORL-XEN-02
       check_command                      check_by_ssh_xentop!nagios! 
/usr/lib/nagios/plugins/check_Xencpu.sh! /root/.ssh/id_rsa
       }

James

>From Nagios server

nagios@nagioserver:~$ /usr/lib/nagios/plugins/check_by_ssh -l nagios -H 
172.16.31.2 -C "/usr/lib/nagios/plugins/check_Xencpu" -i 
/var/lib/nagios/.ssh/id_rsa
"OK:CPU%= 3"


command_line /usr/lib/nagios/plugins/check_by_ssh (1)-l '$ARG1$' (2)-H 
'$HOSTADDRESS$' (3)-C '$ARG2$' (4)-i '$ARG3$'
check_command    
check_by_ssh_xentop!(1)root!(2)ipxenserver!(3)/usr/lib/nagios/plugins/check_Xencpu.sh!(4)/root/.ssh/id_rsa!


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