(I'm replying to Vynce here for both his threads, but do check out his other thread; it's been very helpful)
I've got a lead on this with some repro steps from a fellow who noticed something similar in WriteRoom for iOS. At some stage under certain conditions, the Dropbox sync seem to be 'touching' each file during sync which can change their last-modified date.
I'm still running the repro steps under a few different network speed conditions, but at this time I don't have an ETA on a potential fix or a totally reliable workaround that I'm happy with just yet (sorry). My apologies for the radio silence on this, I had been away, twice, without internet access over the last 2~3 weeks and I'm still working through my email inbox.
It's not 100% the same issue as per your descriptions (the files had been successfully synced before without changing their last-modified stamps) but it seems to be related enough to work with.