About 10 days after my fertile window started i began a brown discharge that lasted for 5 days. it stopped for a few days and has now begun again.?

Not sure: I assume that the brown discharge is less than a full period...If so then if this persists from cycle to cycle evaluation would be appropriate. Most common reasons would be anatomic (fibroid or polyp) or hormonal (hypothyroid or luteal phase defect [controversial]). Usually evaluation would involve ultrasound, possible water sonogram and some hormone blood tests. Good luck.