This is my situation:

I want to increase my vertical, so I want to do squats to train my leg strength. I want to do them with free weights, but my dad wants me to do them on our bowflex. I can almost squat all of the weight on the bowflex. According to the bowflex I am squatting 300+ lbs. But that's ridiculous because I can't do a pistol. (at ~140) Any thoughts on my situation?

I'm not sure about this... but isn't there some difference between pounds of resistance and actual poundage? And how does "squatting" on the bowflex work? How are you situated on the machine for the exercise?

Yes there is a big diffrence in resistance, and real wieght. I use elsastic bands and my bowflex when I workout. I personally prefer resistance then freewieght, its smoother and the farther you push, the harder it is.
I dont like the bowflex for my leg strenth though. I do my squats without wieghts, but I sometimes use the elastic bands as well, they help.

(note that these elastic bands are not yoga bands, but are the heavy duty bands made out of surgical tubeing, one of my bands gives up to 80lb resistance, and you can add bands if it gets to light using the d-rings and hooks that are on the handle.)