It could be MC is analysing for HDCD content, if you haven't turned all that off. It only does that for 16bit 44.1kHz files I believe.
I saw some cda files appear in my Removed Database Smartlist today, and then disappear shortly afterward. I have no idea why that happened. I just assume MC is checking stuff, and for certain actions, touching the file changes the Date Modified.
If you can find something consistent between the files, maybe the answer can be found.
If you turned on MC logging and set a large maximum size (don't set an unlimited size - it could get big!), then when you observe a file being synced that you haven't touched, save the log and search for the file name in it. You should find what MC was doing with the file.