How does preventing the filesystem from writing timestamps solve anything? We're talking about the 'boring partition' having timestamps that suggest that you haven't used it in months (i.e. really old timestamps), when there is probably evidence elsewhere that you have used it (e.g. emails that you've sent since those timestamps).

just write false timestamps to the FS saying it was used more recently?

Or scramble them altogether. Every write to the filesystem through Truecrypt's driver results in a completely random (but still valid) ctime/atime for that file.

I can't readily think of any Windows processes this would break.