How long are the crankarms? How tall is she? Is her knee bent more than 90 degrees at the top of the pedal stroke?

If the pain is behind the kneecap, but in front of the femur, if seat height is the problem, it's more likely too low than too high. A millimeter or two can make a big difference there.

There's an active thread in the Health Issues section about kneecap tracking issues. What you're describing sounds just like the patellofemoral pain I get.

Myself, I prefer non-floating cleats (Look Keo at the moment). Yeah, it took me at least 100 miles before I was done tweaking them to where they felt just right. It meant short rides at first, and a couple of roadside adjustments. And still the occasional tiny tweak 1400 miles later as my muscle balance changes.

To me, using floating cleats seems analogous to wearing clothes that are too loose instead of finding something that fits. But that's just me.