Hi,
Actually we have seen this before, and seems to be related to the AP history, and data integrity, after doing AP upgrades.
Not sure as to the actual steps that gave rise to this situation, but our suggestion is to backup AP data, Run Data Integrity, and then do a Period End to flush old (very old) transactions that are still sitting in the Current Transactions file into the AP transaction history. For the cutoff date choose a date that is say 90 days ago from your last month end, and don't clear the AP history (unless you are comfortable with the clearing date). Normally, the situation of not running the Period End means that the site doesn't like to clear history or are unsure of what the Period End will do to the History clearing prompts.
Most situations that we have seen had not run the AP Period End or Year End for a while, so doing this function should flush the old transactions out and will fix the stub details from the cheque run.
Happy Holidays!
Brian