This past fall, I bought a tri-bike (QR) and again got fitted. Road that bike on the trainer all winter with the shimano pedals and had knee pain all winter. I even went back for a fitting specific to this issue and we adjusted the cleats some but no help long term. Finally in an act of desparation, my coach suggested that I just put flat pedals on the bike. So I went to walmart and bought a set of $10 flat pedals and within a few rides the pain was gone. I could now ride for an hour pain free.
I looked at how my feet were sitting on those flat pedals and I tended to be a bit toe out. I rode on the flat pedals for 2 months and last night I put the PowerTaps's on my tri-bike on the trainer, adjusted the cleat so that it was a bit more toe out and rode for 45 minutes. Almost immediately the pain was back in my knee.
Summary: Left knee pain when clipped in, no pain when using flat pedals. Bike or type of pedal (shimano or powertap) doesn't matter.
As you can imagine I am frustrated and looking for suggestions.