I had increased Multiclone's work pool queue yesterday to try to deal with the idles (which were caused by the problematic user). Unfortunate side effect of this seems to be increased stales. I put the work queue back where it was before. Give it a shot again, and things should be back to how they were before?
I gave it another go and I'm afraid it's still very high.
Grand Total : [1049.77 MHash/sec] [164 Accepted] [16 Rejected] [9.756% Rejected]
This integration of the solo pool as a backup (with blocking calls! one malfunction and everything is borked!) causes more trouble than anything else... My local bitcoind flaked out and needed restarted, so the pool crashed for about 30 minutes just a little bit ago.
Have a couple different longpoll push mechanisms to try that can hopefully fix the stales issue.