If I've had genital warts for 3+ years and they haven't gone away is there something wrong with my immune system? I haven't tried any treatments yet. Don't smoke, live healthy live style and just a a full physical that's was all clear.

Warts. Warts can persist for years since they are in the dead skin layer where your immune system is unable to reach them. Aldara (imiquimod) cream may help or cryotherapy.
Silly. Wherever did you get your ideas? See a dermatologist for diagnosis and treatment of genital lesions. What are you waiting for? You can be treated. You should be treated. Persistence of warts is NOT a sign of immune deficiency. Are you stating you had a "full physical" and did not discuss genital warts?