I am able to reproduce the shutdown problem (USB peripherals and
trackpad work though)  on a T43 with kernel 2.6.31-7-generic. I tried
the 2.6.28-15-generic kernel and did not encounter this issue.

This appears fixed on the 2.6.31-8-generic kernel.

-- 
karmic shutdown failure Thinkpad T40
https://bugs.launchpad.net/bugs/381134
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