Has a Doctor seen the dots?What did he say?

There is a form of Celiac that is called dermatitis celiac ie skin reactions when someone eats gluten.  Have you tried a gluten-free diet?

You should consider getting another doctor, or as someone recommended see a naturopath as well. In general, eczema can be dry or wet (weeping), and the child tends to find it itchy, meaning they often scratch at it. Keeping the skin moisturized is very important and of course if you can identify the cause even better. Often it's dairy, but it could be gluten, soy, or anything that your baby is reacting in an allergic way.

Another consideration is flat warts, as they can be skin colour. Children can grow out of them. Here's a site to confirm if it fits: http://www.skinsight.com/child/flatWart.htm. I do recommend you have a naturopath or an alternative health practitioner who'll offer you way to improve your child's health to perhaps out grow this susceptibility to the virus and not just to treat it with medication.

Hope this helps.

Oh geez, after all the comments what could it be then?  From my perspective it may not be allergy but rather heat rash.  Here's what I found to help with your assessment.  http://www.nlm.nih.gov/medlineplus/ency/article/003259.htm  

I'm seeing our pediatrician next week. Would you like to email me a photo that I an show him. Who knows, this moron could have some good insight.  :D
 (ninjagurl77@hotmail.com) 

Who is your baby's pediatrician?