#### SOLVED!!!! ######
I had a similar problem. I´m using Joomla 2.5 + VM version 2.0.22b
My problem was that when a product has a discount + prices modifier (type DBTax) + personalized fields (for example an extra of 20€ if you want your product inside a really nice box) the discount also was afecting to the price of the choosed personalized fields.
So for example if the product costs 100€ and has a 10% discount + you choose the nice box for 20€ the calculation that is done is -> (100€ + 20€ ) - 10%
For me the correct calculation has to be (100€ - 10%) + 20€
I solved that doing some changes on administrator/components/com_virtuemart/helpers/calculationh.php
Hear by I attached my modified file so everyone can check the changes. Just look for the lines with "BY WOOP" due the changes are allways lines just below my comments
My comments are in Spanish but I hope that comparing the original file with my modification it´s easy to see the changes I´ve done

I hope that this will help others developers that might be facing the same sition I do & if Milbo thinks that this functionality it´s more logic than the one that it has now he could include it on the VM project (or at least create another calculation rule that works as the one I´ve modified for DBTax).
Wish everyone to have a great day!!
[attachment cleanup by admin]