I've applied a fix to the as directed by mine77 and blocks appear to be unlocking now, payments are being sent out.
I will need to investigate how the pool software will handle the crediting the "orphaned" blocks, if it does at all. It would be very painful to reverse engineer the database to determine how to fairly payout hashrates per-block.
It sounds like mine77 is manually calculating the payments the be made, so he might have some tips for you.
Stop by the slack if you're not on it already