Also check if directory attributes have no Read Only flag. This was a mistake in Updater's decompression code, that extracts all files (and dirs) with that attribute.
BTW
Updater will up, as soon as i write new crossplatform GUI version, and add some more useful features.
your installer has problems. I can't install it because it says it can only be installed on machines that have YaPB installed already, and clearly i do. Why can't you just put the actual installer like KWo does. Your current installer is really annoying. You can't choose where to put the files through the installer and it's just really annoying. You have to let the firewalls let it access the internet and stuff.