I heard something similiar Adrian, and tried the time pedals, I must say I hated them – seemed to make things worse for me but, we are all different!
After exhaustive trying of pedals, I found that Shimano cleats, that were properly set up for me (slightly bandy legged) produced the best trouble free results.
I would have a good look at your set up, do you wear down your normal shoes to one side, is one area, and cycling shoes, I cannot use Shimano or regular Specialised, Sidi, as they have a bias built into the sole, which loads up my worn medial knee joint.
The position of the cleat, too far forward or back may cause a cramped or extended knee action – there are many possibilities, and in my experience it takes time if you excuse the pun, to find what is causing and is best for you.