I've been thinking about this one for a couple of days. Your doctor has already checked for the obvious reasons, so it's a bit of a puzzle. I do have one idea, but it's a pure guess, shot in the dark kind of thing and as I'm not a doctor, you should take what I say with a grain (or two) of salt.

In my experience, a lot of the medications that suppress your immune system has a tendency to increase mucus production - as far as I can tell, it's one of the reasons that upper respiratory infections (sinus infections) are so common with that kind of medication. Your sinuses go into overdrive, then get inflamed and before you know it, you have this lovely stew of crap festering in there. I'm wondering if some variant of this side effect is what's happened to your lungs. According to a webpage I found that teaches children about anatomy (click here), the bronchial tubes go into your lungs and help clean out the dirt and germs by depositing mucus. As well, there are tiny hairs called cilia that sweep through your lungs to clean them out and smoking destroys those tiny hairs. So maybe what happened is that the mucus from the bronchial tubes has increased and because you smoke, it's harder for your system to "clean itself out". The good news is that if you stop smoking, it doesn't take very long for the cilia to grow back. You already know that smoking isn't a smart thing to do, all smokers do and still we light up - it's why it's called an addiction. I can only recommend that you kick the habit - I quit five years ago and it didn't take very long before I felt much better. HealthCentral has a stop smoking site with tons of helpful information and tips to help you quit. When you're ready, go here.

That said, I could be full of hot air. I don't have a medical degree and I know very little about the respiratory system aside from basic anatomy (although that website for kids was very enlightening). I'm sure the specialist will be able to help you.

Good luck and please let us know how you're doing.