I can do body squats fine (lots of popping, though). I've worked up in weight (though not quite from empty). One week I'll be able to do semi-heavy squats (not even my bodyweight) with no problems and then the next two weeks I can't even add much more than the bar before the knife-in-the-knee. Both knees have the issue, and not simultaneously. The physical therapist says I'm a bit pronated, so I try to account for that in my posture. I tried all the stretches and exercises I was given. It's not like I'm doing things that my legs aren't used to. I'd been doing leg exercises, including squats for a long time. It's just that when I get to about 85-90% of my bodyweight on squats, it'll only be a week or two of no problems and then for the next two weeks I won't be able to do anything.

I do deadlifts, and they usually go just fine except when I've messed up my knees with squats, in which case then my knees will die during deadlifts too. Every time I tell myself I can get back into squats gradually I come back demoralized, and it poisons my other workouts too.