Don't use your "pant's inseam" as input, it won't work. To get an accurate inseam length, this is what you've got to do. First, get a friend, spouse or sig-other to help you. This is what you will need:

A good tape measure
A wooden dowel/piece of a broom handle (about 18" in length)
A small bubble level.

I recommend that you do this in running shorts, or the like. Tape the bubble level to one end of the dowel. Standing in your stocking feet, with your back straight and upright as possible, hold the dowel between your legs (front and back) and pull up on the dowel until it is firmly against your "sit bones". The level will help you make sure it is, well...level. Now, have your partner make three, accurate as possible, measurements from the top of the dowel to the floor (do this on a hard floor, like the kitchen, as carpet will throw you off). Average the measurements and use the result as your input and you will get your actual inseam. Do this and then try the bikefit program again, you'll be amazed.