In reply to gethin_allen:
sounds like a fit issue, try to find a bike shop that will do a pedal only fit (assuming the rest of the bike fits and you don't want a full on bike fit).
Are your legs the same length... if you sit on a table and let them hang loose do your feet hang in the same way?
If you hang a plub line from just below your knee cap: does it transect the pedal axle? see second image here:
http://bikedynamics.co.uk/fit02.htm
There are so many variables (cleat position front to rear, side to side and angle, using wedges for pitch, possibly varying crank length if your legs are also different, saddle forward/back position and height, pedal/cleat float, pedal width etc) that you can change that it's worth having an expert look at it for you. Also a lot of cycling symptoms seem to have causes a lot further away from the problem than you might think.. for example the knee pain you describe could be more related to saddle position than to the foot interface.