Don't make the mistake of assuming that this is a fluke thing simply because you've been riding for months without issue. I've been riding for almost 6 years now and over the last 2-3 years I've had to address some fit issues that showed up only in specific circumstances, and only after a few years of riding.

My biggest issue was that my left knee would develop a pretty nasty pain on really long rides that involved lots of climbing. Always maintaining nice high cadence, so it didn't seem to be simply an over-use or over-stress injury. Finally I came to realize that only on especially long climbing days I spent more time out of the saddle, preemptively even, from the start of the ride to mix things up. Riding out of the saddle results in each of my feet leaning inward a bit at the end of the power (down) stroke. By installing some cleat shims under just that foot, I slightly changed the cleat interface angle enough to keep my foot from collapsing in as much and within weeks ( continuing to ride) my knee pain had gone away. That was maybe 9 months ago, and I've been riding pain free ever since, even on long mountainous days. Just Sunday we rode about 94 miles with over 12k ft. of climbing, and didn't have a lick of pain from the knee.

If you're having sever knee pain, chances are VERY high that it's a fit problem, and I highly recommend finding a good fitter who knows how to properly address foot/pedal/knee issues and make some changes. Otherwise, you may end up drawing this pain out longer than you'd like.

Good luck, and report back what you find...it's always helpful (or just interesting) to hear peoples success experiences with pain resolution.

-Jeremy