I have experienced what I think you mean MK, for me it was caused by having my hips too closed.
By closed I mean that my saddle was miles above my bars, in a very agressive position - this caused the trouble at the top of my left thigh as my left leg is slightly shorter than my right. I don't know why it causes the problem, but I know that raising my bars, and thereby opening my hips, sorten the problem.