Thank you to Rob from Holland who (not only donated to BleachBit but) reported this bug. When deleting the Places database in Firefox version 3 using BleachBit 0.4.2, it's not possible to save new bookmarks. The bookmarks disappear when Firefox is restarted.
A Mozilla knowledge base article gives the solution. If you suffer this bug in BleachBit 0.4.2, close Firefox and run this command:
The explanation: Firefox tries to reconstruct the missing places.sqlite file from the JSON backups.
The fix is applied for BleachBit 0.5.0. For older versions, you may apply this patch.