Dude, I am in the same boat and have been since I was a little kid. I've always been heavily muscular (legs especially), but I never used it as an excuse. I was always the top runner in my high school and on my college team, and that was enough for me. I wrestled a bit and was a gymnast, and my wrestling coach once called my thighs "freakisly muscular" so I use that to describe them to this day.
I was never fast at the mile or below but seemed to excel at the 5,000 but then had a dropoff as the distance went up from there. My marathon times are not indicative of my shorter distance times for example. This could be a result of my not having a thin build, could be that I didn't train properly for the marathon (I know I could do better and will do so in the future); I don't know for sure what the answer is.
Bottom line though is that people are built differently. Training and eating right doesn't necessarily turn you into a lean-looking runner.
I'd use your performance more as a guide if you are in the right thing or not. When I could not catch up to the 85 MPH fastballs they were throwing in 8th grade, I quit playing baseball. If you are running fast, then so what of your build. There are many rail-thin runners who can hardly average 8 minutes per mile in a 5 mile race, and then there are some bigger guys with about 20 pounds of FAT to lose who run a 5K in under 16 minutes.
The magic is in the runner and not the body type.