I've chimed in on a couple of threads regarding the Bakers Cyst that formed at the back of my right knee after a difficult ride. In addition to the cyst (bulging of knee fluid), I had some major knots in my lower hamstring and upper calf. That was 7 weeks ago...
After an initial two weeks of doing nothing, I started riding a little, and going to some spin classes. I've been gradually increasing level of activity, and going to physical therapy sessions. Problem is, every time the therapist would loosen up the knots, they'd come back after riding. I've been stretching, got a massage stick, and problem continues.
Finally, last night, the therapist that has been working on me asked the senior guy what he thought. He immediately diagnosed the problem as actually starting up on my glutes. I got some serious application of their elbows to my gluteus maximus, and the senior guy did some excruciating release work with his thumbs on my hamstring. I told them that I felt like hamburger when they got done.
The senior guy told me that if I do my stretches every day, and continue with therapy, that the problem should be resolved in about 2 weeks. I hope so - I'm getting tired of having one leg at 80%.