My conditioning is also very uneven. Running would be trivial (I ran a half marathon at 7:55 min/mile a couple of days ago), I could also manage sit-ups just fine, would fail on push-ups (but not by much) but can't even do a single pull-up.
I do notice I weigh 25-30 pounds less than my friends that are same height and waist size. I'm 6'3" and when fit hover a little under 170 lbs, while everyone else is 190-200. I think it's a distinct lack of muscle.