Hi,
I am sure you must have done some of the analysis already on these points but it does not harm to do it again:
1) Check the Customer Master and check the Tax Category of the Customer to make sure that it is maintained as 0;
2) Check the Tax Record [MWST Tax Condition Type normally] for whichever tax table you are maintaining it for exists
3) Check in the Condition Tab in Pricing Details if you are finding the assess to the Tax Records happening for the Customer and Material combination.
If you find any of these three as the smoking gun you should be good.
I do not think personally that if the issue is only with one customer that this is an upgrade issue. Even otherwise, Tax related stuff has not changed in anyway between those versions.
Get back to me if you have any questions.
Thanks.