Ok this is the most maddening thing ever... I used to make software and this is not intuitive...

If QB finds the right invoice match on the initial matches found (14 total)  and you click match, everything works and the fee and deposit match and are attached to paypal bank...

If however you have to click "find other matches"(most of the time for me), than for some reason it unlinks the fee and deposit, putting the deposit in paypal bank and the fee in undeposited fee... and they are not easy to link back up...

Not only that, but I just figured that out after 100s of transactions because it should have worked with the match function...

(on a side note you should be able to link a customers paypal account to your customer in QB so you only see that customers invoices)