I've now seen another list where it didn't want to pick the item I clicked on. It was an autocomplete list in the tag editor, kept picking the one above (which was also the first one).
Sync appears to be working smoothly, except sometimes the text doesn't show in the status bar. You can see the X, but there's nothing next to it. Also, if I cancel a sync I almost always get the message "Unable to abort background process. Recommended action is to restart MusicBee." This happened in 2.x, too, though.
Something doesn't seem right with the "preserve folders and filenames" option. My storage path is ...Music Sync\, and with the full naming template I had the tracks syncing to Music Sync\Music\<First Letter>\... With the preserve folders and filenames option (showing Music\*), I'm getting Music Sync\Music\Music\<First Letter>\... Shouldn't the * pick up where the naming template for the library picks up? (And likewise for podcasts and audiobooks)