Great, glad your sorted.
To me it is not "bizarre" - you need to understand that the B2's interface accesses a database file that describes what is on your hard disk rather than looking at the hard disk itself. What "Scan Disk" does is rebuild this database file so that it matches the actual currant content of the hard disk. Some things you do to your hard disk contents mean that the database and contents become mismatched and your B2 interface seems not to be telling you the truth.
Thus a periodic "Scan Disk" followed by the "Save" process (which makes sure the new database is written to disk) is a good think to do as a first port of call when you have issues.
Fred