Negative pregnancy tests but no periods for 2 months?

I've been on the combined pill for about 3 years and ever since then my periods have been regular as clockwork! But I have now missed 2 periods and this has never happened before. I've had some brown discharge around the date my period is due, which I usually get but then it just stops as quickly as it started. I've done 3 pregnancy tests which have all come back negative and I've also had 2 nasty bouts of cystis within 2 weeks of each other which I treated with antibiotics. Confused as to where my periods have disappeared to, any ideas what this could be if not pregnancy?