You may want to check out ; http://www.sportsinjurybulletin.com/archive/knee.php
that website has a lot of really good info. on all kinds of injuries.
Here are a few things I found:
Aikido knee walking and seiza puts your knee joint oftentimes in traction. This is not usually encountered by people and is something new. It is completely different and will tend to 'soften' up the joints. Arguably this is by design...but you can definitely do this to excess.
For instance, it is possible to introduce too much laxity into this (or any) joint, or asymmetrical laxity (i.e. too much slop in one side/axis). Be careful. If you can rule out an acute injury; i would gently suggest that there may be a mis-use pattern in movement. Listen inside your body to see if things are fitting as they are supposed to. Approach the pattern like a koan to solve.
Also; it seems (again barring an actual injury) that the onset of knee pain in a lot of cases (I AM NOT A DOCTOR!.. this is IMO) is due to asymmetry in the insides to outsides of the leg. The adductors (i.e. the muscles on the inside of the thigh that move the legs toward the body's centerline) are too tight and the abductors (i.e. the muscles that move the leg outwards away from the body's centerline) too weak.
Less common but totally within the realm of possibility are likewise to have such length-tension imbalances between front and back (i.e. hamstrings/quads). Other imbalances also can exist. Generally ;stretch everything that is too tight. Know that you will have a blindspot for the muscles that are the most tense...untill they start to soften up too.
Foam rolling on the TFL and adductors really can't hurt. Scratch that. at first it will hurt like a bugger; but it will help...there's lots of info on that.
Figure this out. Listen in your body. Heal it up.
Good Luck. you only have the one set of wheels.
p.s. go to the doctor if you can, if you suspect injury (i suspect you do suspect it). Good Luck.