Read the articles at this link
http://home.hia.no/~stephens/exphys.htm
I think you will begin to understand what is going on. Especially read "Understanding Interval Training".
In a nutshell, when you get fitter roughly 2 things happen:
1. Your cardio system (heart etc) gets fit, ie is capable of transporting a lot more oxygen.
2. Your muscles grow and capillaries develop to deliver all that oxygen.
Problem is, #2 happens a lot slower than #1 so you can easily get a scenario where your cardio system works really well but the muscles are trailing behind. So you don't run out of breath but your legs run out of puff. This is also demonstrated by a very fit runner getting on a bike for the first time - after 5 minutes of climbing he's ready to hurl his breakfast despite being very fit. It's because his musles aren't trained to cycle.