What is desperately needed here is indexing. shares.time should have an index, to avoid a table scan.
Actually shares.time is indexed already. The table is over-indexed for such high transaction velocity. He needs help. I've offered my services via PM 3 days ago during the previous stats incident, no reply. I do this for a living and would appreciate a little more professionalism put into the backend.
EDIT: Today's results seem to confirm my theory that the auto-trade algo is affected by database I/O issues. We came out the stats freeze with very little exchanged BTC.