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I haven't seen you mention it anywhere, so did you try a BIOS / firmware update? I've had similar bugs on multiple Thinkpads before and they were universally cured by an update.

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Thanks for the suggestion, but I've updated the BIOS multiple times. It didn't fix anything.

What version of Ubuntu? If it's 12 then you might need to do what I did for my new PC a year ago to get the latest drivers:

https://wiki.ubuntu.com/Kernel/LTSEnablementStack

That fixed the only issue I had which was with the 1 Gig ethernet. Now I'm on stock 14 and of course it has all the newer drivers already.

I've tried 12.04LTS, 13.10, 14.04LTS, and now 14.10. Sometimes upgrading, sometimes from a clean install. The current issues with my ThinkPad are due to bugs in the latest drivers.

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