My niece takes the pill to suppress her periods, but if she's under some unusual stress, either emotional or physical, she has a period that always starts with brownish discharge. Emotional stress is usually something like an upheaval in her love life or work and physical stress can be something like starting a diet or a new exercise program. This has been going on for 15 years. For her, stress = a period, even if she's been taking the pills exactly as indicated.

Stress can cause menstrual problems by disrupting what's called the H-P-A-G hormonal axis. G stands for gonads (ovaries in women) and A stands for adrenals, the most reactive gland during stress. The bodily disruption seems to over-ride the pill's suppressive powers.

But like the other posters, I think it's a good idea to see the doctor prescribing the pills if you haven't done so recently.