Not a virgin, but pain during intercourse?

I am 16 years old and I lost my virginity about a year ago. Now I have a different boyfriend, and we have had sex 3 times. The first time (about 3 months ago), it hurt slightly because I had already had sex once before. And the second time (a week after the first), it didn't hurt at all. And since the second time we had intercourse, we hadn't had sex for about 3 months because we wanted to wait until i was put on birth control pills. I just finished my first pack of Lo Loestrin FE birth control pills, so yesterday we decided it was safe to have sex. When we got the condom on, deciding to be double-safe, he put his penis inside of me. I immediately made him pull out because it hurt so badly. It had felt like i was losing my virginity all over again. We tried doing it in a different position and it still hurt! I'm concerned because I'm not sure why I had that pain. It's not like it was our first time having sex. And at first I had thought maybe it was because we hadn't had sex in 3 months. But before, since I lost my virginity, I didn't have sex with anyone for about 7 months until the first time me and my current boyfriend did 3 months ago, and it still didn't hurt that badly then! Does anyone have any idea what this pain could be from? Maybe a pill side affect? Thank you!