If you use the same profile folder with places.sqlite with both versions then you shouldn't do that. It is quite possible that the 4.0 beta versions update places.sqlite and that using that updated file with an older version has corrupted places.sqlite.

You should always use separate profiles when testing other (beta) versions.

See http://kb.mozillazine.org/Testing_pre-release_versions

See also http://kb.mozillazine.org/Locked_or_damaged_places.sqlite

You can try a validation check of places.sqlite.

Copy and Paste this code in the Code field in the "Tools > Error Console" and click the "Evaluate" button to cleanup and compress the places.sqlite database file.

Components.utils.import("resource://gre/modules/PlacesDBUtils.jsm");PlacesDBUtils.checkAndFixDatabase();

This shouldn't be the case. The problem existed before the beta was given to the public for testing

Edit: Just to be sure I ran your code and it said it's ok and tried to backup again. It didn't work.