by Emma Richardson.
That is just so strange. It was screaming cache to me but if you can actually see things being updated, there about has to be something funky going on in the database somewhere.
As Ken mentioned, make sure that you don't have two sites accessing same database. I would also check that the user referenced in config.php has the appropriate permissions...
Is the database on the same server as the moodle code and moodledata? Could there be some network deal going on where the database is disconnecting sometimes? How are you performing the backups? Through the gui or through cli?