Looking at how much you're being charged is not enough. You have to look at your transaction history from SunPass to see if you were being charged based on your transponder or from your license plate.
For example, my transaction history from Virginia E-ZPass shows whether I was charged based on my transponder or my license plate, but either way, the charges are the same. The fact that I have an E-ZPass account means I get charged at the discounted rate, regardless of how I was tagged. If my transponder doesn't get tagged properly, they look at my license plate and link it to my account automatically.
Just for shits and giggles, could you try putting your transponder the right-ways-up and see if the "Go SunPass" illuminates when you pass a checkpoint?