Defect Rating on partial returns?

So I was just reading on another post about sales tax and it said that your defect rating will go up if you give partial returns? It also says PayPal will cut you off if you are giving partial returns?
I have many listings that are a flat $2 shipping with a $.50 more for each additional item. This works fine if the buyer buys multiples of the exact item or they request an invoice before they check out. The problem I have is a buyer will buy 4 different items listed with this same shipping and it charges the full $8 instead of $3.50. So i have just been going back into PayPal and giving a partial refund of the difference of what the shipping should have been,  $4.50 in this example, and leaving a message that say "over payment for shipping" in the note to buyer field.
Is this wrong? It has been working fine. I guess i'm now confused over this...

wow I just gave a seller back his shipping because priority mail took 3 weeks he opened a case I was going to refund his money but the item show up today so now i have a case that was opened and i was nice enough to refund priority shipping because I felt that he paid for priority but recieved sub standered service from USPS He never asked for any thing. GO figure nad now im going from a top rated to a above standered ARGH THIS IS INSANE
also I think this might be a way to push sellers to free shipping
I just spoke CSR and they are checking into it
wow cancled transaction now count against you OMG i have 5
but they were because the buyer requested me to cancel transaction UGH!!!!!!
this is going to be a fun couple of months