Extended period on Seasonale, what's the deal?

I've been taking Seasonale for about three years now, and have been taking some form of oral contraception for a couple years prior to that. My periods have never been extremely consistent even on the three-month regimen, but I've never dealt with an extended period like the one I have currently. It's been around five weeks since my cycle began. Nothing has been consistent about it as far as bleeding goes. It shifts back and forth from brown to bright red. It will stop for an hour and then come back with a heavy flow.

I went to my gyno a couple weeks ago and he didn't see anything physically unusual. He just said to wait it out. Last week my primary doctor found that my thyroid hormones were off and put me on two drugs to regulate the issue. One symptom of hypothyroidism is irregular periods. However, after a week of taking the medications nothing has changed with my cycle.

Basically, I'm confused, generally frustrated, and wasn't super satisfied with my gyno's answers. I was wondering if anyone has ever had a similar experience on Seasonale or the three-month regimine in general? Should I consider switching pills or contraception methods? Has anyone generally had an experience with an extended period, and what was the outcome?