What type of bedding are you using?
Have you had any blood work done?
Can you post a picture of the areas? Use the paper clip icon if you have a PC or if you have a Mac please use Photobucket and post the link. Joan
I can tell you that you need to go back to a solid substrate as the repti Sand and calci sand is very dangerous. This will give you an idea about Sand as a substrate: http://www.beardeddragon.org/articles/impaction/?page=3 . I suggest using a solid substrate like tile, cage carpet, slate or paper. Sand can also cause skin problems and cormeal ulcers in the eyes. The sand is sold as a safe edible substrate, but it is not and actually very dangerous along with the other loose substrates.
What you are describing under the scales is Vesicular Dermatitis. It is also known as blister disease. It is usually an infection that is deep seated under the scales. This is a link about the problem: http://www.reptileexpert.co.uk/blisterdisease.html
If the Vet you had seen was not one that sepcializes in Bearded Dragons, I suggest that you see one, as this needs to be treated with antibiotics and may need avitamin supplement to booster the immune system. I am going to give you links for Herp Vets in Australia: http://www.wolfwood.com.au/rept2.html As it is going to take a hands on exam to properly diagnose and treat this issue. Joan