I had symptoms similar to what you're describing earlier this year. Mine came from my desk at school that had a support bar right at knee height. I kept knocking it in the same place for months on end. I'm not talking bashing it, just every now and again I'd tap/thump my knee on it. One day, there were stars. I'm talking like take your breath away invountary vocalizations, what the hell was that pain. It seemed to be coming out of the blue, but it was probably just building up the damage (bruised tissues right over the bone).
I took anti-inflammatories (naproxen 500mg twice daily) for about a month and made sure not to touch my knee to that bar and the pain went away. In you case, I'd consider staying away from kneeling, and a neoprene knee brace just for padding in case you forget.
Course my medical advice is probably worth what you paid for it,

so do with it what you will. Probably a good idea to see the MD just in case, though I'd bet he'll prescribe anti-inflammatories for a couple of weeks and tell you to come back and see if it's better.
spwg