BF is not a good place to get medical advice. You could have strained your knees, you may have damaged them and have bits floating around in them, and a number of other things could be causing the problem.

If lowering the saddle helps, I wonder if you're not hyperextending your knees or if there's something about your stroke that is torquing them in some strange way. On the other hand, a couple inches is a huge adjustment. It's probably worth studying your stroke and see what you're doing and seeing exactly what causes pain and what doesn't.

I'm suspicious of the saddle theory because unless you've changed your seating position, I can't see how that would affect your knees.

In any case, don't just tough it out. Otherwise, you could really screw things up and be off your bike for awhile.