Akash, yes, I think may be right. Upper traps are definitely contributing to the headaches though I don't know if they are the primary cause. I don't have regular pain in the traps themselves and can't tell if they are spasming.
But if I compress the UT muscle in the area where the neck meets the body, I get referred pain in the back of the neck. Have been doing self-massage of these areas for a while hoping to resolve trigger points, but with no effect so far.
It is possible that lower trap exercises are messing with the upper traps too so I was doing less of those recently. Again without much effect one way or the other.