This should really be a comment not answer... but I don't yet have enough rep to add a comment !
So in this link on the Ubuntu Wiki there are instructions for installing and using the various sensors with Ubuntu. This should enable you to get more info as to what exactly is causing the overheating. Other than that, you could test on a live CD to see if you still have the same problem (it may be a WUBI specific issue that needs a bug report).
In fact a hunt and I found this page on ubuntu brainstorm, and lead me to the launchpad bug report
You should add your info to the report, or open a new bug if you think it is different enough.
Did I mention that I don't have enough reputation to post comments or links !
The thread also has some workaround details.
If you are a linux newb and need more help, just put a comment into this thread (or better still update your question).
Also I would highly recomend the ubuntu forums (if you are already a member), although I get the impression that a lot of the forums folks hand around here also.
sorry I feel that I haven't really helped out much - its a bit of a naff answer, keep us updated with how things are going...