Not sure if you will heed this information but here it goes. I ride a lot in my LHT with a ton of weight usually on it. I never have had problems riding in the past 6 years that I have used clip-in style pedals. MY position has almost never changed nor has my riding style. Well beginning of this last summer my knee started to ache an I had no idea why. I gave it about 3 weeks and it just got worse to the point of having a hard time walking. I went and had a MRI done, and the doctor was sure of the fact that I had torn my Meniscus. We got the MRI back and it was fine, it was just inflamed. Well I still couldn't understand why it was hurting, but I also was still riding my bike *I am stubborn* Well I flipped my sandals over one days to make sure the cleats were tight and something just didn't look right. Upon closer inspection.... My cleat was off just a hair from center *where mine usually are* at first glance you can't even tell. Well After I fixed that... it worked like a gem. Knee pain was gone in a couple days and all was better. So it may be something you want to look into.
Cheers,
Coconut