Adding my frustration to this thread. In my case it is not due to a fee, it is simply a credit card processing timing issue that happens frequently. 

Scenario: 

Day 1: credit card sales are 1,000. The following day the credit card processor deposits $990. QB does not find a match and since the filter on matching is capped at <=990, I cannot match to it. 

Day 2: Credit card sales are also (for ease of illustration) $1,000. The following day $1,010 is deposited in my account. I can match that to the $1,000 and make an entry to post the extra $10 to a credit card payment clearing account I have set up. 

If I could have likelwise matched the day 1 990 tdeposit o it's corresponding sales record, I would have had $10 balance in the clearing which after day 2 would have netted to 0.

This isn't difficult or incorrect accounting. Very basic. Why can't I do this? All the workarounds are so much more time consuming and add to the growing pressure to find a different bookkeeping product.