I had the same problem with my laptop in terms of thermal runaway and the fans not cutting in although mine is a HP-Compaq and not Thinkpad. Basically what i found out was that it was due to buggy DSDT tables and so the ACPI consequently not working:
Here are the rough steps that i took to remedy the problem:
1. Updated my Bios. I am told in the vast majority of cases this may solve the problem as the vendor releases new DSDT tables with the Bios upgrade that address issues in linux
2. This didn't work for me so i compiled a custom kernel with a DSDT table i downloaded from here:
http://acpi.sourceforge.net/. Now be careful with this because the bios has to match the DSDT table that has been published.
3. Hope this solves the issue and you get no more ACPI errors when booting.
incidently what errors do you get with regards to the ACPI when booting.
If you do chose to compile a custom kernel (not that hard really, i did it and i'm crap with linux I used this guide
http://www.recompile.org/index.php4?page=kernel2.htm which was ace) then try installing the ACPI modules into the kernel. I don't know if this helps but it might.
To tell you the truth, recompiling a new kernel with custom DSDT table did help a little with my thermal control, but what i would suggest is seeing if there's an option in bios to have fan on with AC power, and invest in an external USB fan!!!
Hope this helps
