Same issue, it's soooooo frustrating and it's irritating our customers. Here's what happens to me.

1. I receive a client check for Jan invoice on Feb 5

2. I make Jan invoice paid and add check number

3. I deposit the check

4. Quickbooks downloads the deposit and matches it to the Feb invoice and marks it paid.

Now if have two invoices marked paid by the same check creating an accounting nightmare and confusing our customers and now I have to go dig through deposits and figure out what's going on. For software that has been doing accounting for years thus is utterly redicuous.