Sage 100

Customer on Sage 100 2013 JobOps switched inventory from FIFO to lot back in February. Had issues from the start and JobOps applied some patches, but there are still scenarios where the item transaction records do not match the lot serial transaction records. The IM transaction totals seem to be the correct ones, not the lot serial. Anyone else having this problem?

Followup on this: (1) I created a report for the dates where they were re-entering the lot qty after changing the valuation to match up the IA transactions with lot transactions, and it all matched up. (2) I created a report to list all the lot transactions and then match up the item transactions. It found a few (< 10) mismatches, almost all on make to stock. (3) I then created a report listing all the item transactions since 2/28/14 and the matching lot transactions. This found quite a few where there was NO corresponding lot transaction. Any ideas?