First i got the order in admin panel, and it all looks good, amount paid seems correct and well, happy with it!
So minutes later mail from PP come and telling me that "you have received payments from XX, and just briefly looking at it, i notice that the amount seems much smaller that order amount, so i double and triple check, and YES there is a difference

It seems customer have paid for the products alone, and somehow got a big shipping cost for free...I'm like WTF.

Browsing the event log i find this line:
PP_STANDARD :: TOTAL PAID MISMATCH! XX.00
Also, i can't seem to reproduce the error, i have tried many times with my own test user, shopping the same product and amount and then clicked complete the order, redirected to PP it all seem fine, correct products and the total amount.
What is going on?