I had a related problem with Dropbox. Some files uploaded from my Linux machine were not synced to my Windows machine. Later I narrowed down this problem to images being saved from Twitter, which have URLs ending with ":orig". On Linux, Firefox happily saves such images as "blahblah:orig.jpg", whereas on Windows it uses space instead of a colon. And of course Dropbox on Windows would completely ignore filenames that contain colons and tell that the directories are synced, when they obviously aren't.