Ah, yes. This sounds familiar. My issue with the 1650 transparency adapter is that it tries to put a 4x5 negative in a 6x6 frame.
I have not found a solution for this phenomena either. I have tried epson forums, FAQs and lots of internet searches. Uninstalling and reinstalling the software does provide a temporary solution (for about two scans), but then the problem does return.
I fear the solution to this problem is GAS. That's the abbreviation for Gear Acquisition Syndrome. Yup, a new scanner should fix this right up. And with typical GAS problems, it's easy to buy, tough to pay.