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Hi, it sounds like your hormones are off-balanced due to the starting and stopping of the pill. It could take a few months to regulate. There are many others on this forum that have experienced what you are describing. The brown discharge is most likely old blood. Best wishes to you. tmv
When I went on the pill I had the same thing happen to me. It really sucked because I didn't want to have that kind of peirod. That was how I knew my period was ending when i did have one and to have the light brown gunk for a period was really hard to tell beginning from end. It lasted a could of months and then I got back to normal flow and wished for the light stuff again. Relax.
I talk to my gyno about it and she said that is normal and by cycle 3 it should be back to normal. I hope this helps.