[Saxtus]

I don't remember anything about backup in XBMC UI. Or you mean Video Library Export/Import?
Anyway, I'd recommend to backup your Video DB physically by copying your %AppData%\XBMC\userdata\Database\MyVideosXX.db files to another location, then do library export, delete your Video DB files, then import your exported library for XBMC to create a clean Video DB file.
Or please wait for some time. I'm going to do some test myself (as soon as I find time) and then post specific recommendation if there will be any.
Though, I'm afraid, export-delete-import is the only way to migrate back to the standard XBMC database format.

P.S. Eduard added support for MySQL too - now the DSplayer database is stored as a separate database in MySQL, thus (theoretically) providing compatibility between different XBMC instances that use a central MySQL database.
I'll post more specific info later (again, I need to find some free time to do this).

I did the steps you told me and the problem remains.
But I have some new piece of information now, after some testing I did:

Bookmarks at video category, maintained correctly, even without restoring the database.
Bookmarks at LiveTV recordings (that triggered my previous post), is still the problem, even after re-importing.
Newly created bookmarks at LiveTV recordings, seems to be saved correctly.
Tried both your's and panni's builds.

LiveTV bookmarks must be stored elsewhere...