Hi there, sorry to hear that your beardie's eyes are bothering him. We didn't get to go over your setup with your yet. Could you fill us in on the brand & type of UVB you're using? Is it a coil, compact, strip fluorescent or mercury vapor bulb? How close is the bulb to the basking spot? Are you using a white or colored basking bulb and what is the wattage, the size of the tank would be helpful too. What type of thermometer are you using to check the temps and what are the temps? What is the substrate on the bottom of the tank?
My first thoughts about the eyes is that you are either using a coil or compact UVB which are dangerous to their eyes. Or, he got a loose substrate in his eyes. If it is from either of those 2 ideas, you can flush his eyes out with Saline solution eye wash, that seems to help give some relief. Please let us know what the vet had to say when you get a chance.