I do remember thinking that myself but it does do it correctly when you look, just done one now.
If you enter a positive fee amount the difference becomes twice the fee total because essentially if you have say a Β£3 fee thats missing from the invoice amount and you enter a positive "fee" amount like Β£3 this appears to be more income not expense, so the difference is now double.
If you enter -3.00 it will resolve to the correct total. Presuming the invoice was Β£100 and the fee was Β£3 in this instance.
Just make sure the rest of the fields are as mentioned above but this is much quicker and easier than the other method posted above which does seem to get suggested a lot but if I had to do it that way I would just invoice in Paypal directly and enter them as sales receipts when I do an upload. Keeping a monthly/quarterly sum of my paypal fees to enter at some point as an expense.
