That is very strange. Searching the forums a bit I turned up this post with some thoughts. Did you use the
sqlite3 command to dig into the db by any chance? Sounds like that was the root cause of the issue there.
Also alternatively have you considered using the mariadb addon instead? I switched a while ago and it got rid of a lot of start-up performance warnings for me so it might be a win-win to just take this opportunity to switch.