Time machine does not do indigo SQLite databases properly.
May I suggest you use indigo utilities
http://forums.indigodomo.com/viewforum.php?f=184. It has fixed 2 databases issues. (have not tested it on more situations. Talk to John from the Netherlands, he just went through it.
I also suggest
strongly to use the backup utility included. It will make a copy of the database every x hours and THEN time machine will back up the copied database properly, or you can keep 1..5 copies - see config.
Karl
Kartl