There is a possible fix for this problem in the newly released
2.6.34-rc3 linux kernel. From the changelog:
Daniel T Chen (3):
ALSA: ac97: Add IBM ThinkPad R40e to Headphone/Line Jack Sense blacklist
There should soon be a PPA of this kernel RC available at
http://kernel.ubuntu.com/~kernel-ppa/mainline/
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On IBM Thinkpad T40 series, the Headphone Jack and/or Line Jack inputs need to
be muted in order to hear sound at all.
https://bugs.launchpad.net/bugs/303789
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