That is odd. Even if he was not eating a lot of salad, with the T5 and dusting, he should not have MBD (Assuming that is what it is). There are two types of T5 though: one for desert use (High Output) and the other is for jungle use. Make sure you have the HO one.

With the mesh lid, you should still be okay. There is NO plastic covering in your fixture, right? Some owners buy the Wal-Mart fixtures as a diy, and forgets to remove the plastic covering.

If the fixture is fine and the lights are fine, I am out of answers for you. I would strongly recommend you to go to the bearded dragon dot org forums for help. They have a section specifically for questions like yours regarding beardie illnesses. And of course, your new vet will confirm what he really have going on. The first things you post along with your question are a pic of your tank, enclosure size, temps, lights and dusting schedule. Good luck.