If I pg_dump that database then create a new database (e.g. "tempdb") and upload the dump file (thus making a duplicate) then the same query only takes 190ms !! Vacuum, vacuum analyse, and vacuum full analyse does not seem to have an impact on these times.

Damn, for some reason I didn't read that you had already tried vacuum full. In that case, I can't explain it except perhaps you aren't vacuuming properly, or the right thing, or it's a disk cache thing.


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