I've sustained multiple injuries in the past in my left knee, and get the same sensation about once a ride. Fortunately I ride fixed, so it's easy for me to do this, and I don't know how hard it would be on a roadie. When clipped in I pull my leg up against the downstroke, letting the pedals 'pop' my knee for me. I'm much more comfortable after that.
If you can swing health insurance, next time you see your GP you might want to mention it. If it's just that 'knuckles need to be popped' sensation I wouldn't sweat it too much, though if you're feeling other types of discomfort or getting swelling you ought to make an appointment to get it checked out.
Also, consider your pedal choice and think about whether you should have a little more usable float. I like Eggbeaters because they're fairly floaty and adhere to my "can kill a bear with it" rule, but I hear Speedplays are very comfortable pedals.