You are correct...  What I find works, is when it comes through the Bank Feed with the "incorrect amount" that doesn' t"match the Paycheck is to do a FIND MATCH...

1. Check the box for the check that it should have matched to

2. and slide the bar on the Bottom that says Resolve post the amount of the difference as a negative or positive depending what the difference is. and

3.post it to Reconciliation Adjustments or Payroll Adjustments with an explanation of why it is different. 

That is the only way I have been able to remove the duplicates.  Let me know if this works for you.