When I have it hurts?

I have been with my current boyfriend twice. He isn't big by all means. He is more on the smaller side. I know it isn't a lubricant problem because I always get really wet. I do have HPV, but it is a low strain and i really don't think it affects anything. I have noticed that I hurt while we are having and after we have had , and the pain will last up to a day. I have had other relationships and they never hurt like this. I have been to the doctor sin I have HPV I get recheck every 3 months, and everything is ok accept that. Could the HPV be the problem???