Answer: Yes, Windows modifies its filesystem (that file) every time it boots.
Workaround: Once you have Windows configured the way you want it, make a snapshot. After the initial backup of the main pvm file, Time Machine will then back up the much smaller snapshot backing file rather than the big file. Once your snapshot backing file starts getting big enough to be a backup problem merge it back in (delete the snapshot) and then make a new snapshot.
Disclaimer: I haven't tested this with Parallels (I turn off Time Machine backups and do manual backups of my pvm's from time to time), but it worked this way under VMware Fusion.
Last edited: Jun 27, 2012