I would take the pills, they know what they are doing. Are they giving you something to jump start your cycle?
If they thought you were pregnant, they would have given you an ultrasound...take the pills and hopefully you will regulate =)
I've been hearing a lot lately that dr pregnancy test have been coming back as a false negative and the women actually been pregnant. If you really feel that you are pregnant, I would take the pills and I would demand the ultrasound. There would be no harm in the ultrasound, but if you were indeed pregnant those pills can harm the pregnancy.
Blood test would tell you for sure if you are pregnant or not since it tests the amount of hcg in your blood vs urine. But at 3 months or 12 weeks you should be showing positive on a regular test if you were indeed pregnant.
What are the pills? What are they saying it is for? Are they birth control or fertility drugs such as Clomid?
I had a very very irregular cycle when I conceived my first born. I would get my period any where from 2 weeks to 2+ months apart. We didn't have any trouble getting pregnant.
Then my cycle still wasn't normal because I was breastfeeding and I got pregnant twice-the first time I miscarried and I am pregnant again.
I would definetly insist on an ultrasound and any other examination that will help identify what is going on. Have you ever missed periods before? What is your normal cycle?
You should suggest an ultrasound. Even if you're not pregnant, it would serve to rule out any ovarian cysts that may be preventing you from ovulating. Are you taking anything to help regulate your period? See your doctor soon. Don't worry if it's a cyst; most are benign and treatable :) Good luck.