Late period, thick discharge, not pregnant?

Kelly
My last period was very late, by over 2 weeks, when I'm normally relatively regular--within 28-33 days.  I'm not on birth control, and my boyfriend and I normally wear a condom but he's pulled out several times when we don't have one on hand, so naturally I thought I might be pregnant. I took two pregnancy  that were negative, then my period started (and it was definitely my period, not spotting or anything) 
My period is very late yet again, and the same things are happening: more thick discharge than normal, and a week ago it was brownish and I had some spotting. We've used a condom every time we've had sex this month, so I doubt I'm pregnant.
 
I was having some weird, brown discharge over the summer so I went to a gyno, and they checked my thyroid, for infections, etc., and it all seemed ok. 
 I was pretty stressed last month so thought that might be the cause, but my life is pretty steady now so I'm left wondering why my body is doing this. I'm in my 20s and my period has been regular since high school. 
Anyone else experience this? What is going on?