Before your BF adjusted your saddle, was your knee in front of the pedal spindle or behind it? Did he adjust your saddle height to account for the change he made to the saddle's fore/aft position? How much would you say that he changed it? Where does your knee hurt? Have you been giving yourself a long warmup on the trainer? Are you potentially just pushing too big of a gear?

For me, KOPS is not optimal in that I like to be a bit further behind the pedals. A good fitter will tell you that KOPS is just a starting place; there is some flexibility in the rule of thumb. That said, I think there are potentially a few other things that might explain your knee pain.