You don't say how much higher the new position is compared to the old position. Sometimes too radical a change in saddle heigth can cause knee problems. The other thing that comes to mind is working on your knees on a hard floor. I know this from experience. If the problem does not clear up on its own in i week or so, I'd then begin looking at the position on the bike.

On second thought, if you have recently increased your mileage by a significant amount, say, 30% or so, this could also cause knee problems. Good luck with the diagnosis.