If Hide hidden files and Hide protected operanting system files are enabled, these files are not compared in synchronization. It would be interesting if you had an option in the sync panel to sync all files, including hidden ones.
And there is a strange bug in synchronization. If the options to hide hidden files and system files are enabled, empty folders are compared even if they are inside a directory which has a filter to ignore it. For example, if I use a filter by full path to ignore the directory C:\Games\* and all its files and folders, synchronization will still compare the empty folders in that directory.
Obs.: I checked that this only happens when the "one way copy" option is enabled and the directory to be ignored is in the destination.