I am having this same problem, and the solutions proposed by Quickbooks do not work for me.  The only way I have figured out to fix it is to manually include the fee reversal as a "negative expense" in the refund transaction (so if the refund is -$100 and the fee reversal is $3, you will include the $3 as a negative in the expense, for a net refund of $97).  It will give you an error saying that the transaction balance doesn't match what was imported, which you have to say ok to.  Then you need to exclude the separate line item for fee reversal that quickbooks imported in the wrong direction.  Your quickbooks balance should match your paypal balance after that.

This is probably not the "right" way to do this...but it's a workaround until Quickbooks figures it out.