I also had trouble getting a deep breath when running. I thought perhaps I was developing asthma and was going to go to my doctor for tests. I would describe my breathing problem as not being able to fill the top part of my lungs fully. At times, especially if it was humid, after a bit of running I could hardly breath without stopping.
I started taking 50mg of DHEA (for other reasons), which you can get at most drug stores. Within two weeks I noticed my breathing was significantly easier. At first I just thought it was a coincidence but that effect has continued for 2 years now with no relapse. If you decide to try DHEA, make sure you get a brand that says "verified by HPLC" that means the DHEA concentration was verified by high performance liquid chromatography in an independent lab. Some brands have been reported to have no DHEA in them at all. You should probably get a DHEAS test first before taking DHEA to check your levels before and after taking.
You didn't say how old you are. If you are over 40, it is possible that this effect is also caused by low testosterone. Do you have any other symptoms like muscle mass loss, irritability, memory problems, muscle/joint pains especially in the legs, or unusual fatige?
[This message has been edited by orion (edited 10-12-2003).]