You just have to pass the correct adjusted price to paypal so the totals add up.
On line 55 of confirm.php you have:
$WA_PP_ECO_Do_itemized[0][$nextIndex] = "Amount" . strval($cartIndex+1) . "";
$WA_PP_ECO_Do_itemized[1][$nextIndex] = "".$esEmailCart->DisplayInfo("Price") ."";
it needs to be:
$WA_PP_ECO_Do_itemized[0][$nextIndex] = "Amount" . strval($cartIndex+1) . "";
$WA_PP_ECO_Do_itemized[1][$nextIndex] = "".($esEmailCart->DisplayInfo("Price")+$esEmailCart->DisplayInfo("colourPriceInc")) ."";
Same concept on the pp_confirm.php on line 98. You have:
$WA_PP_ECO_Do_itemized[0][$nextIndex] = "Amount" . strval($cartIndex+1) . "";
$WA_PP_ECO_Do_itemized[1][$nextIndex] = "".$esEmailCart->DisplayInfo("Price") ."";
it needs to be:
$WA_PP_ECO_Do_itemized[0][$nextIndex] = "Amount" . strval($cartIndex+1) . "";
$WA_PP_ECO_Do_itemized[1][$nextIndex] = "".($esEmailCart->DisplayInfo("Price")+$esEmailCart->DisplayInfo("colourPriceInc")) ."";