Im so confused.

Okay, this is going to be a long one and I doubt many people will read the whole thing but that's okay, I just need to get it out. Towards the end of May I broke up with my boyfriend of a year then I missed my period, there was light bleeding but not a lot or for very long. I made an appointment with the OB and they ran a lot of test, I wasn't pregnant but my thyroid level weren't good. I had levels that were twice as much as they should be. I'll now be a medication to stabilize it for the rest of my life. I've been on the medicine for about a month and a half, I had my period last month and it was normal and everything was fine. I'm two weeks late for my period this month and I have had unprotected sex twice since my last period(I already know, Stupid Sarah. I took a home test and saw a faint line and so I went back to the OB and she said it was negative. But I still haven't gotten my period, could I be pregnant and it's coming up negative? And is it possible that I'm just not fertile? I don't worry about it every second, and I'm not really stressing over it I just feel like I don't know what is going on with my body. Any insight would much appreciated and if you made it to this point you deserve a freaking cookie.