ok. I deleted the files in the WARNING messages.
now I went over again your How-To in 
http://www.thinkwiki.org/wiki/Install_Ubuntu_9.04_(Jaunty_Jackalope)_on_a_Thinkpad_T400#Active_Protection_System
It was workin as it always did for the first time.
I didn't want to restart my System, so I just tried to remove the loaded 
modules:
 - sudo modprobe -r hdaps
 - sudo modprobe -r tp_smapi
 - sudo modprobe -r thinkpad_ec
then I tried to reload the modules:
 - sudo modprobe thinkpad_ec tp_smapi hdaps
FATAL: Error inserting thinkpad_ec 
(/lib/modules/2.6.28-11-server/kernel/ubuntu/misc/thinkpad_ec.ko): Unknown 
symbol in module, or unknown parameter (see dmesg)

dmesg returns:
thinkpad_ec: Unknown parameter `force_io'
- lsmod | grep hdaps
returns nothing

now I repeated the compilation steps again:
 - sudo make load HDAPS=1 FORCE_IO=1
hdaps: driver successfully loaded.
 - lsmod | grep hdaps
hdaps                  18648  0 
thinkpad_ec            15000  2 hdaps,tp_smapi

-- 
error loading tp_smapi module
https://bugs.launchpad.net/bugs/311336
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