I have a similar problem.
I'm on the pill "Ortho Tri-Cyclen" I've been using it for 2 months and my last two periods have been normal but I haven't gotten it yet this month and I have found think brown discharge I've read that it could be a different type of period. But I'm not sure because earlier this week it stung when I pee'd but thts gone away now and now I have this strange discharge. Does this effect your sex life? Can you have sex while this is happening?
I don't know wats going on does anyone have answers?

I was also on that pill for a while and like ANY birth control pill, your body has to have time to adjust. If you've only been on it for 2 months, use a condom if you have sex.

The discharge could be "old blood" which may indicate that your period is coming. However, that with the stinging sensation you felt during urination should be evaluated by your doctor. Anytime you have sex, there is potential for the stinging sensation you mentioned. Your body can become irritated from the friction of intercourse and the stinging sensation might occur... but should never last long... maybe just one trip to the bathroom.

I suggest calling your doctor to find out if he/she would like you to come in for an exam.