Some DMV staff are really stupid and arrogant. My wife also have trouble with them when she tried to use an I-94 with a revised series number on it (hand written by Custom officer due to an officer mistake on prior I-94). She delayed her driver's license renewal until she re-entered the US recently.
Take it easy, you have no way to argue with them as they know nothing and refuse to learn about immigration related issues. If possible, try to use another DMV office if you can.