I would suggest double-checking if you are following the "golden rule" of shikko: Keep your feet under your weight and your weight over your feet.
You may be learning too far forward (or leaving too much back behind you) - putting too much weight on your knee(s) and thus stressing the joint in question. Aside from that, should pain be present, and should you have actually worked your way through the flexibility issues regarding the toes, ankles, knees, and hips, you might have an injury - which could be anything from as small as an ingrown hair to some kind of tissue or joint strain (or more). Double check your knee(s) for redness, tenderness, and/or inflammation, then treat accordingly.
I would also recommend adding Ikeda's video/DVD "Za" to your library -- which covers such topics and provides drills and exercises as well as some key pointers toward improving your technique. You can purchase "Za" at www.bujindesign.com
. If you may find it helpful, we also have some videos on our web site that show many tenkan maneuvers from within Suwari waza. Follow the link in the signature below.
Hope that helps. Good fortune with your test.