I'm having same issue-customer overpaid.   the credit memo created, used the  "use credit to give refund" feature- check created, customer:job is correct on the check AND STILL the report for  Accounts receivable has the credit on it- not applied! ! 

What can I do    this is stupid.

Frustrating when you can do a transaction with pen and paper but can't get QB to do it!  been a user for over 25 years.