I have 1200+ files in my hd, mostly videos, which I backup to an external drive. I sync these files with WinMerge. I have noticed that in one specific folder WinMerge now detects the 4 mp4 files there as different, having each file in the hd exactly 122 bytes more than they originally had. As far as I can tell the videos haven't suffered any modification. The only operation I remember having done is moving the files to new subfolders (which I did in both sides, obviously). There's actually no problem so far, but I can't figure out what has happened here and it's driving me crazy. It's a Windows 7 64 bit machine. The rest of the files remain identical including 2 avi files and 6 plain text files in the same folder.
Are the files really getting their size changed? Make sure you are comparing their sizes with the same program, that the program does not round file sizes to different units, and that you are seeing actual file size, and not "Size on disk", which accounts for compression, sector alignment, etc., and could be different on different disks.
If they are changed, how to find out which program is changing them? For a generic, "scientific" approach, you could use SysInternals Process Monitor to watch activity on a specific video file after you move it. Then you would which process is responsible for the change.
But as a practical hunch, I would say that the video files are getting their metadata changed by some Video library program you have installed. Could be Windows Media Player. These programs typically index every media file you have, and they have options for updating files with media information they grab from the Internet, to check digital rights, etc. This sort of information could be getting written to the file.