I upgraded two Win2k workstations that belong to the users that print checks, have no problem. But if they print to a different printer, it would be off. It might not have anything to do with MAS, the reason I say that is because I don't have security access to this module so I don't know if there's any settings or it's a Crystal Report. Check your printer settings or drivers. I am able to change printing margins on these laser printers that we use for this purpose.
I am no expert, but I am just giving you a feedback on the same senario as yours and that I didn't have to do anything with MAS90.
Hope this helps.