Snapshot Plugin: Restore has broken my site

Good I am only beta testing my site at the moment with limited users as the Snapshot plugin simply broke my site! I did a backup of all data and made a restore afterward. Now, many entries are messed up (e.g. widgets missing, classifieds and events plugin 404 errors, no cubepoints levels, ...). This is what happened:
The restore process stalled with the wp_options table at 70%. The server log told me there were several duplicate key names in it. I don't know if this is related to the actual problem. So, I switched to the Snapshot Admin section again and all the snapshots are gone. I rescanned them, the latest one did not appear (even it is in the directory).
So, I left the Snapshot admin area and restored the wp_options.sql file with phpMyAdmin - the file was from the latest snapshot. I didn't receive any error during the import but still the site is totally messed up. Probably there is nothing wrong with the plugin but the wp_options table itself.
But what I can't explain: why did everything work fine before I ran the backup and restore? I didn't made any changes to WP between the backup/restore.