Solved by a Lenovo BIOS upgrade which is now available for X61t machines as
well. See here:
http://www-307.ibm.com/pc/support/site.wss/document.do?sitestyle=lenovo&lndocid=MIGR-68005
The following changelog line is relevant to this bug:
Version 7SET23WW (1.09)
* (Fix) Unexpected interrupts from the USB controller may occur. (BIOS)
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kernel disables irq after 10 minutes
https://bugs.launchpad.net/bugs/126369
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