Possible Cyst, need some help please?

I have had a pain in my side on and off for the past 8 months. When it first started they did a sonogram and found nothing. Just diagnosing me with acid reflux. The pain started again and was rushed to the ER thinking it was appendicitis, thankfully it wasn't. They thought it was possibly my gallbladder or maybe a cyst in my ovaries, so they did another sonogram and a CAT scan. Both came out clear. Now i have always been late on my periods, even with the pill, i stopped taking it almost 2 months ago, but i haven't gotten my period in a month and half. I took a test which came out negative, and just started the pill again a week and a half ago. Don't the doctors MAKE you take a test to see if your pregnant before the give you the pills? They gave me them anyways without telling me the result so Im uming it was negative too. My mother keeps scaring me into thinking Im pregnant, but i think it's more serious then that. Im scheduled to see an OB/GYN in the next two weeks, but i would like to have a general idea of whats going on sooner.