You must be missing something from your backup or the backup process missed something. Not positive with that.
The 1054 error could be due to missing db updates. The current release you say you have is 1265. Your executables are 1316. You should always check for any updates between the db and the release, so updates from 1265 to 1316 are found in the svn under /utils/sql/svn/ and I see 3 with 1 being for bots and is probably the cause of the error. Check the changelog.txt file too cuz sometimes the sql updates are in there.
Backing up the database has a new requirement with the addition of some views/method. It now always requires the -R switch for mysqldump to pick those up. Not sure if that is causing your buff issue, but thought I would mention it.
EDIT:
I thought I would mention that you probably could avoid this by not going to a fresh db each time. The drop_system.sql file does not delete user tables, and once you've run that then you run the db update for 1265 plus any svn updates and all should work.
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