I'm not an expert at dialing in cleats, but one thing you might check is how you naturally orient your foot (i.e., toe-in, toe-forward, toe-out) when you stand and when you pedal on your flats. If your cleats are forcing your foot into an "unnatural" position, you're going to feel it in your knees. The float in the pedal will allow some range of motion (typically between 0 to 7 degrees, depending on design), but that may not be enough to accommodate your natural posture.

Some folks argue that you want the cleat straight even if you naturally toe out, because that will "train" the knee to get closer to the frame (which is, in principle more efficient)… but it's sometime hard to teach old knees new tricks, and can do more harm than good.

I'm sure others will provide better advice. And it might help them if you describe where your knee hurts (back, front, inner side, outer side). Good luck!