I get the same thing on my folders too, if you look at the files within the folders, they will all be checked as read only. That is, if you selected the option to "apply to all sub-folders and files as well" (or something like that when you selected the read only check box).
As for Mp3Tag I got that sticky-tag issue too, sometimes I had to run the remove tag operation twice (only once, 3 times for one song) to get certain tags completely clear. For me, I saw no correlation between the sticky-tagged song and syncing issue, it just seems like some of my songs had two sets of tags on them. Good call not doing all your library at once and testing it out step by step. Whenever I retagged whole sections of my library with the copy, remove, paste method, I made sure to keep the files I was working on selected, I don't know what happens when you loose focus on them and then select "paste tag" without having all of the songs in question selected first. I'm not too inclined to find out.
Thinking about the playlists: You're referring to the titles of the playlists, and that seems to be a listing inconsistency between the software and device. Looking at the differences between device totals and on-computer totals, have you deleted files off the computer version of the playlist while hoping the computer would resync it the updated playlist to the device? When I make metadata edits to videos, I have to manually remove the video from my device and my collection and then re-add them to back to both places to get the software to recognize my changes. Try deleting the playlist off your device and then resyncing the updated playlist from your computer. It's not auto sync, but hey, this thread is about syncing issues. And I'll concede, manually syncing a lot of playlists could get tedious. I don't think the playlist section has a scroll indicator (you mean scroll bar?) because none of the other sections do, they're always organized alphabetically. Or do you mean the playlist section doesn't even have the large alphabet character to orient you? Other than my quick list, I've only made one playlist. Finally, I do agree that being able to simply view an artist by song would be a nice feature to add ("view all songs") right below the "play all" option. More often than not I remember a song name, not an album.
Good luck trying the retag operation, I am really hoping we have a valid work around.
Edit: If you have playlists that are on your device but not in your software, then I believe the only way to remove them, other than editing your registry to
make your Zune a portable hard drive, is to reformant your device. I wish that weren't the case and hope some one knows another way of removing playlists (and songs for that matter) that show up on the device but not in the software.
Zune MVP
Contributor, http://www.insidethecircle.net