Seatpost could have slipped a cm or two - unless you measure / have some sort of marking to indicate, you don't know that it's remained constant. Happens slowly of course, unless you get into an abrupt crash.

Try gearing down and seeing how it works, re-examine the post height, if all else fails try omega-3's and MSM/glucosamine. Everytime I have knee pain it's always due to saddle height and gearing...