I have had some of the same issues in the last weeks---bought a new bike & raised the seat too high, which led to lots of posterior knee pain, which has mostly gone away after a few weeks rest & lowering the seat.

What is of more concern to me now is some seeming weirdness around the patella whenever there is lateral movement (eg. when I leave my feet planted and twist my body to do something like look over my shoulder). The patella seems to drag across something and there is either a sharp pain or it kind of goes weak. It reminds me of a cartilage tear I had awhile back. Hopefully nothing like that. Anyway I have been to the doctor (thanks Japanese socialized medicine!) and there was nothing funny on the xrays.

At this point I am just taking things easy, but anyway back on the bike.