I have experienced the same when trail running.
I can pretty consistently reproduce the symptoms on downhill stretches when running distances that are much longer than my regular runs, when starting to hit the trails again after not running for a while, and when running downhill at a faster pace than I would run uphill.
The following is my hypothesis, meaning I don't have any published facts to back this up:
When going uphill we are fighting gravety in a pretty static way. It is not likely that we would go any faster or for longer distances than our muscle-mass permits.
When going downhill on the other hand, we have momentum that our muscles have to slow down. Fightling gravety becomes less static and more dynamic, especially with steeper slopes and higher speeds. We can keep going even when our muscles are fatiguing, and we can go faster than our muscles can effectively slow down, which passes the stress of slowing down on to our skeletal system (mainly our joints.) This can be compounded by heavy heal-striking (less cushioning by our muscles) and a heavy pack (providing a larger mass, which increases the momentum.)
My advice would be to take downhill stretches at a much slower pace (on my trail runs I am MUCH slower going downhill than uphill!), avoid steep slopes until you build up the specific muscles you use for descending, don't take as much stuff when moving on steep terrain and transition to a midd-foot-strike when you notice your knee is hurting (a word of caution: practice this! If you are a heavy heel-striker this can be very tiring for your calfs and you can damage your achilles-tendon if you don't strengthen it first.)
I take this kind of pain pretty seriously. To me it is a sign that even though I have the conditioning, I am missing the muscles to do what I am doing when my knees hurt.