Pain in the back of the knee (like in the popliteal area) is a pretty classic sign of a high seat ... which doesn't necessarily mean that your seat is actually too high, especially since your fitter thinks it's still too low. More likely it's just too much too soon.

Half an inch (12 mm) is a LOT to change seat height all at once. If I need to change mine, I'll go 3 to no more than 5 mm at a time. Ride at least 100 miles to let my body adjust, then go the next step.

Since they're already sore, be extra careful. Ice today if you can (no more than 15-20 minutes at a time, and not too close to your evening workout) and definitely after your run. Try putting your seatpost back up maybe just 2 mm lower than it was for a week or so, then go the next step and see how it feels.