I have been working with Victoria on this and made some progress. I've run Inventory Reconcile on individual PIDs and that fixed some items. We also noticed that the SQL query, for some reason, was showing mismatched ATYALLOC and LOTATYALLOC, even though they should be the same? This appears to be what is screwing the report up.
I will try and run Inventory Reconcile on all the PIDS and see what happens.