Problem with PS1.6 = "Warning xxx paid instead of xxx"

[BlizzardUK]

I am really stumped on this one. When people pay for our 2nd shipping carrier, using our Agile PayPal module (it may or may not happen with the official PayPal module too, I am unable to test), and it will show up with the wrong price in the back office, our email invoice and the customers email invoice. The price that shows up, and the carrier, is our 1st carrier. So for instance, if the customer wants basic postage they can choose our 1st carrier at £1, but if they want a signed for delivery then they can pay £3 for postage. But when people select that option, and pay via PayPal, then their invoice, our invoice, and our back office will show the 1st carrier name and price (£1). Even though they are correctly charged the full amount (£3) and the correct amount was shown when they clicked submit. In our back office it shows up as the wrong price, with an error that says ""Warning xxx paid instead of xxx", insert whatever the price was. 

The even stranger thing is this only happens with the PayPal module, not with our credit card module. The credit card module processes the transaction perfectly with the correct carrier info and price on the invoices. So what I need to work out, is why does the PayPal module make it select the 1st cheaper carrier as postage price (and carrier name), but this doesn't happen with the credit card module. Also why does it show the correct price when they click submit, it is only post transaction that the wrong info shows up. 

I have tried changing the rounding up info from item to line, but this doesn't make any difference. 

Any ideas ? Thanks.