For steel and Aluminum, the answer is fairly easy. The stiffness of the bar is directly proportional to Young's modulus for the material and the weight of the bar is directly proportional to the density of the material. Steel is 3 times as stiff as Aluminum and also about 3 times as dense, so the natural frequency should be very close to the same. But for the Nylon, you should get a much lower natural frequency, about 1/5th of the other two. Something is wrong.
backing up what jerry says, here's a blog article we recently wrote on frequency analysis: http://www.hawkridgesys.com/blog/simulation-resonating-harlem-shake/
noah, are you running with restraints or without restraints?
are you running with any loads?
it might be worth posting your files just to have them double checked.
Thank you both for your insight. That is really interesting about Aluminum vs. steel and I see that relationship now. I ran the nylon vs. steel again on a completely new part and got completely different answers. I'm not quite sure what went wrong the first time I tried this.