Adagio Ledger has an option on the batch to 'auto-reverse' the amounts for the subsequent fiscal period. You can see this by clicking the Rename button on any batch. It appears that this option has been set on some batches, and I don't belive that retrieval from sub-ledgers does this.

The next time batches are retrieved, don't post any of them as part of the retrieve process and look at each one from the Rename screen. Do any of the retreived batches have the auto-reverse property enabled?