thanks for asking. funny timing too. I mean, the original problem last year was solved. that was popliteus most likely. but I have something else now in the back of the knee. and this one seems to be hamstring related.
I'm not sure what it is exactly. it's my left leg mostly. no pain at rest, no pain at the start of my runs, but I usually get it at about 40mins into running, it's a dull pain in the back of the knee (it is not kneecap, it is behind knee), and it slowly gets worse if I go on. on stopping it feels very stiff/locked, I have to do something like stretch the quads on that leg to make this "stiffness" go away. a few seconds of stretching left quads is effective at that.
a bit of walking and going up stairs helps too. I think it likes going up stairs because knee is flexed at every step and I noticed it definitely likes a flexed knee in general. e.g. sometimes when it gets really "locked" from some bad movement (sometimes happens during the day, not sure what movement causes this), I find relief by kneeling to keep the knees fully flexed for a few seconds. quadriceps stretching also has the same effect, very deeply flexed knee during quad stretch makes it feel "unlock".
so, after the run all that dull pain/feeling/whatever goes away in a few mins but when it started up about 2 weeks ago it was really bad because even walking was somehow off the next day, along with the dull feeling(not exactly pain).
I then figured out that when this problem started my running style was a bit "off" too, somehow I wasn't flexing the knee much while running - I was jogging easy-ish on a track, 2 days after a hill race(uphill, no downhill in race). then in this run on the track, at one point I started feeling a dull pain at every step at one specific point at the bottom of left hamstring=back of knee. I stopped after a few mins and I was ok, but next day when I went for an easy run, 20mins into the run I ran down a little hill and then it started up and wouldn't go away, and that was when next day even walking was "off". it was no longer a specific point, it was more general in the back of the knee.
anyway, walking is fine now, and I got my running style back to normal(I think..), but some runs are still no good. it seems it does not like downhill running much (I mean it will tolerate it for a while but I think downhill is more stress than flat terrain or uphill running).
OTOH, last run was a tempo run and that was fine, I think it likes tempo pace. slower paces throw it off somehow.
important: I just found out tonight that I cannot easily stretch out the hamstring on that leg with the problem (left leg) because it will feel too painful. I can convince it into stretching out on second or third try but it just doesn't feel right. and it now hurts in the hamstring muscle, it didn't hurt before, maybe I overdid this stretching...?? I don't know how to make it more flexible again or what caused it to be inflexible in the first place. this is what I need to figure out! I'm not sure if stretching is good at this point, as it made the muscle itself hurt afterwards (not behind the knee, but more up my leg). it still hurts, it did not hurt before I tried these stretches.. :bangs head into wall in frustration:
actually my hamstrings were never really flexible, but I want its flexibility back at the "baseline" because I think that would solve the problem! because, I can see that when running, when I swing my leg forward, I feel the pain/feeling right after that, I think it is when hamstring is trying to stretch out a bit before the foot lands on the ground..?? and because it can't stretch out properly, it's pulling on the tendon/tendon pulling on insertion at knee?? I could be wrong in my analysis of the situation though. just guessing, I don't know running anatomy too well.
I tried massaging around but I could not find any painful points/knots. but maybe I didn't look thoroughly enough. 2 months ago in april I had a similar issue on the same leg and then I was able to find a painful spot when massaging the hamstring, and massaging that point fixed it right away, at least it stopped bothering me back then. a difference was that in april it did not hurt during runs, only after runs.
on the whole it's better than when it started but it doesn't want to go away yet.. I cannot do long runs because of this 
I'd be grateful for any tips on getting that hamstring flexibility etc. back to normal! and a few questions, does simple rest solve such a problem or do I need to take other steps too to fix this extra tight hamstring? (I assume this is what causes the issue.) was this stretching a good idea (causing muscle soreness afterwards)?