I know the folks at Bitvise have gone around the block a few times with daylight savings and timestamps as well, so I think they've also got it right.
Rather than working around buggy servers, I think you'd be working around a buggy OS, which I think is a justified exception to make. I can try to complain to MS about this, but experience tells me they probably won't listen. In this case, the operating systems themselves locally report different timestamps on files that a couple weeks ago had the same timestamps. The file's timestamp hasn't changed in either location, but the OS' interpretation of what time that means has apparently changed.
I would just use synchronize timestamps, but this is a large number of files. Some really have changed, and some haven't. I can't just treat them all the same, and separating on a file-by-file basis would take a week.