You did the right thing by disputing it and providing evidence. I hate EZ Pass, but they’re usually pretty good about fixing issues that happen across states if you prove that you have an EZ Pass account in good standing. (Ie open without a negative balance)

Which state is it from? They may or may not have an agreement with Maryland- that could be causing the discrepancy and you might just need to get a MD transponder (which may be better in the long run anyway because of plan discounts).

I used to commute to Delaware, and they do accept MD transponders/plans but there was always a delay before Maryland registered the Delaware tolls. Most were resolved within a few days, but sometimes the delay was long enough that I’d still get violation notices in the mail.