With you and your BF both being virgins and monogamous, your situation is one of the few when I can say with confidence that the areas you describe are unlikely to be HIV. Furthermore, warts do not come and go as you describe. There are many skin folds and skin tags which can occur in the genital area around the bottom of the vagina or between the vagina and the rectum. If either of you had had sexual contact with others prior to your current relationship warts would certainly be a possibility but even so would really not be something to worry about. HPV is the most commonly acquired STD. Over 85% of sexually active women will have HPV infection at some time in their lives. In some HPV will cause genital warts, in others it will not cause warts but may lead to changes in PAP smears. In nearly everyone who gets HPV, warts or otherwise, the infections will resolve by themselves without therapy in 8-10 months. In a very small minority of women, HPV infection can persist and lead to the pre-cancerous lesions that PAP smears detect and which can then be treated.
In your case, warts in the location you describe might not have shown up on your Pap smear. My advice is, if this concerns you, go see your gynecologist and have him/her take a look. At that time would be a good time to discuss receipt of the vaccine to prevent HPV infections. It is highly effective and well tolerated,
The topic of HPV and genital warts is a complex one. I will try to provide some facts. For addition information on this most common of STDs, I would suggest search for other HPV- and wart-related Q&A on this site, as well seeking addition information on sites such as the American Social health Association web-site (disclosure, Dr. Handsfield and I are both on the Board of ASHA)..
Hope these comments help. EWH
As for transmission to your BF, while it is a possibility and something that you would prefer not to happen, should it, as your doctor and I have already said, it is not a big deal.
Finally, I would re-state my recommendation that you get he HPV vaccine. just because you have had one type of HPV infection does not mean that you cannot get others.
EWH