Thanks for your response Amie635, I appreciate your time. It turns out that the colposcopy test was normal :) Guess it was some abnormal cells that healed over time.
The definitive length of protection from Gardisil is still ambigious and unknown. Most research points to five years worth of protection atleast, so the effects may have worn off on you leaving you unprotected right now.
Also it doesn't protect against every strain of HPV, just the four most common (two of which may have been detected in the PAP, the other two wouldn't as they cause genital warts). So you may have contracted a less common strain in which the vaccine doesn't cover.
Don't panic too much if it does turn out to be HPV. As your Doctor stated it is very common and most women encounter the virus at least once in their lives. It has a stigma attached as it is an STD, so people don't talk about it and as it is so unknown it is thought to be very serious and dangerous. As long as you follow your doctors advise you should be fine and free from the virus (be it waiting 6 months to see if your bodies immune system heals the virus itself, or treatment if you have a more seriouse case)