Before anybody gets killed by suspense over this mystery, I will lift the veil of ignorance from the screenshot
The left shows SI, the right side shows the same synching process with another synchronizer from a .7z file to a folder.
Clearly SI misses a few files that are in the folders. This happens no matter what synching option (backup, duplicate etc.) I select. No files or subdirs are excluded. File in question can be dld here http://www.imagemagick.org/download/bin ... indows.zip