I have to side with the DMV.
If there are vision issues, then I'm not sure where you can be upset with them for failing you on it. You said it takes a few minutes for your eyes to focus? That seems like a problem, I would think.
I recently re-upped my regular icense in the fall...I took the same type of vision test. Letters, colors, flashes, numbers in colors, the whole shebang. Granted, you have to be able to focus your eyes fairly quickly on the test, but if you're guiding an 80,000 pound piece of loaded machinery down the road with me next to you, I wouldn't want it taking you several minutes to focus on something.
Just my $.02.