Project related costs posting to different periods

Summary:

We are using encumbrance accounting and budgetary control. When processing invoices or expense reports, the recording in GL and Budgetary control is coming in from the Payables module. The project entries for the transactions should net to zero in both GL and Budgetary Control in the same period. We are seeing that in most cases, all but one line is posting in one period and a debit hitting a prior period. This is manageable in most periods, but at year end we have project transactions failing the import due to the stray debit hitting the prior fiscal year.

Is there a way to have the net zero project costs post to the latest open period or at least all in the same period?