Dual boot access is very problematic (been there

)
1) Time is kept differently by Windows than Linux. (there is a Registry hack that makes Windows keep the BIOS clock in UTC. have not tested this since XP). This can mess up time stamps (which is newer determinations)
2) File names are case INSENSITIVE in windows, so you can have
Windows.epub, Windows.EPUB, WINDOWS.EPUB
all in the same folder, but a Windows user can only see one and Calibre only tracks ONE of any EXTENSION in a folder (and no way to know which was the good one).
The Quality check plugin might help a TINY bib. The Fix section can do something if it is only the Path (folder name) that is bad. I would run this from Linux
Bottom line. Use the content server in READ ONLY access, to access books on your lesser used OS.