Vyapada and Andrew Dixon, thanks for your posts.
Vyapada, my “outside” muscles are certainly stronger and a physio already told me that was an issue with my left patella tracking problems (I get patella pain when I run). Also, the VM on my left leg (the clonky one) is clearly smaller than my right VM. My left hamstring, calf and ITB are also tighter than my right. So basically my left leg is one tight mutha LOL It sucks, cos my right leg is fine.
I’ve been working this tightness and trying to strengthen my left VM, but results come very slowly.
I thought the clonking might be patella related, but when I put my hand to my knee I can feel the ligament/tendon/whatever clonking on the back of my leg, towards the outside.
As an interesting note, I did back squats the day before yesterday for the first time in over a year (been doing front and overheads instead) and my hammies were sore yesterday. I went into the gym for a bit of rowing, and while warming up I noticed that I could squat without a clonk (I almost cried of joy). After the rowing session, when my hammies were warm and supple, the clonking was back again. Hmmmm…so does a sore (hence tight) hamstring actually keep the clonking from happening? Should I not be trying to stretch my hamstrings?
The plot thickens…
Sxio, I have no idea if your issue is the same as mine (although it sounds similar), but I squat ATG, despite my clonking. I’ve never felt any pain because of it, so I just try to warm up a lot to get the knees lubed up and ATG away.
Miserere:
So at the back of your knee on the outside you experience a clonk in the general area of your hamstrings?
Might be… could be excessive rotation of the tibia due to poor control of your biceps femoris. This is outside of my education and experience, though. Give me a couple of years and I might be able to help 
I think that perhaps your rowing session tired out your hamstrings and in a fatigued state they probably couldn’t stabilise your tibia sufficiently.
Check out this picture Illustrations. Fig. 438. Gray, Henry. 1918. Anatomy of the Human Body. - if you’re not familiar with superficial posterior knee anatomy but it seems like you are.
If you’re curious, something you could try is sitting in the position pictured (sorry about the quality and model, I only have a mobile camera) with your hands feeling for your semitendinosus and biceps femoris tendons, and while keeping your foot flat on the floor try turning it to the left and right (i.e. inducing rotation of the tibia) aiming for a strong contraction feel under your fingers . Try to notice differences in activation of these muscles when compared to your right hand (good) side.
This might give an indication if my conjecture is on or off track.
It also makes for a good start at trying to regain control.
(Good) Physios are generally quite adept at helping treat movement dysfunction. If it’s not out of your budget to go see one.
Thanks for your long post, Vyapada (nice pic too :-)). I tried what you said but can’t really tell a difference in how my right and left hamstrings activate. I’ll have to find a physio and hope they know what they’re doing.
Hey,
I was probably completely wrong!
Taking a stab at what’s going on with you without consultation is best left for the experts and even they make mistakes - it’s just too easy to make the wrong assumptions.
It’s promising that they don’t seem to be too different - muscle retraining can be really boring!
I hope it settles down for ya but keep us posted it would be interesting to know how it works out.
