I have had problems similar to what you and the below above poster Sarah describe. My injury can be traced to a very bad ankle turn (laterally) on a trail almost 6 years ago, that I probably didn't have properly heal. In fact, I never had it x-rayed until 2 years later, and the x-ray showed that likely I had fractured a small bone in my foot or ankle (can't quite remember) that changed foot mechanics. My theory is that this changed the tracking of my patella, taking it off line. When I run I get a slow buildup of tightness around the knee during which I can feel my leg lift dropping drastically, and then if I step awkward I get shooting pain under the patella.
I do also get the cracking or clicking in both knees actually, fairly often. Anytime after I just wake up or even just sitting down for an hour. Its not usually painful, but once in a while it can be. I'm not sure how much advice I can give you other than that I would think scar tissue could be a cause of the clicking, and maybe something with the meniscus. I've seen doctors of every ilk, and none have really been able to identify clearly what I might have. Then again, I also have never had an MRI, largely because I have no extra cash for one. Boy would I love to be able to fully run again though, so I feel your pain.