My thinkpad (t43p) recently overheated, after changing the fan and heatsink the 
cpu scaling now works correctly.
It seems the issue was simply that the kernel decided to keep the cpu speed low 
rather than running the fan to cool it down.
This bug report can be closed

** Changed in: linux (Ubuntu)
       Status: Incomplete => Invalid

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cpu scaling not working properly
https://bugs.launchpad.net/bugs/381588
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