Please compress the full original hand history files for a few of these errors and attach them to a support ticket in the support section of the PokerTracker website and we'll check them out. There do seem to be a number of genuine errors in Merge hand histories, but we would like to find and fix any remaining problems importing valid hands.
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Also, has the EV calculations for 6-max tournaments been corrected for the Merge 70/30 payout structure?
Do you actually mean EV, or do you mean the payout structure? Please create a separate ticket about this and include an example where you won, along with the buy-in amount and prizes that were actually awarded. We try to keep the auto detection rules up to date as much as possible.