Migraines can be a side effect of birth control. However, unless your doctor instructed you to take your Seasonique in the manner you are doing, I would suggest not doing so until you've sorted out the migraine issue and whether it's connected (talk to your doctor to find out, especially if you've noticed any correlation between frequency and being on this particular pill). Usually the only time skipping placebo pills for more than 3-4 months at a time is recommended is in cases where the patient has PCOS or endo.
I was always told black/brown blood was old blood and its normal. I would get migraines with certain brands of birth control, so that's a possibility.