How do you prove in a court of law that a.) those timestamps are correct and b.) I have definitely used it since July 2011?

Standard practice is to use the one you don't care about for things you don't care about (which for most people, will be most things. Web browsing, gaming, emailing the aunt, whatever).

Timestamps are going to be at the FS layer or higher, not much Truecrypt can realistically do about that..

Truecrypt does have an option to disable file time updates on file volumes. Also for ext at least, you can mount with nomtime, noatime, noctime and completely disable file times.

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.