just throwing a thought around since I tend to have sore knees too:
You said you make sure you aren't putting any pressure in the stirrups, does this mean you have been prone to pressing down with your feet in the past?
The reason I ask is I have to be conscientious of myself when riding as I will find myself locking my knees or pressing my legs down, even after I made not of it part way through the summer I catch myself doing it a few times a ride
So IF you are/were prone to riding defensively you might still be doing it and just not catching yourself when you arn't thinking about it
Yes I am very bad about it...usually more so at the beginning of the season, my mare slurpee is a little green yet so sometimes instead of nicely stepping over the log we jump half way through or jump over the stream instead of walk...we always go back over and over making sure you do it nicely but I still get alittle tense :(...the mare I was on this weekend is bran new to me so I could of been and not realized...(my girl is nursing a hoof injury and is not ride able on steep rough country until next summer at the soonest )