Thanks for keeping us updated, dstahl.

I've read the previous response and I can see that all possible causes and troubleshooting steps have already been shared with you.

The Custom transaction number feature only applies to sales transactions suc as invoices and sales receipts. 

In this case, it's best to reach out to our chat or phone support teams. They can take a closer look at this to determine why an old check number keeps on showing up when creating new transactions. Here's how:

1. Click Help in the upper right-hand corner of QBO.
2. Click Talk to a human, then type in Talk to a human.
3. Select I still need a human.
4. Click Contact Us.
5. Select between Send a message or Get a callback.

The Community is always here if you need anything else.