It sounds like PFI9 (CTR0 GATE) is trying to drive the signal as well. Try disabling the PFI9 output in software.
If that's not the problem, it's possible (though admittedly unlikely) that your square wave has a very high source impedance, so high that it cannot overcome the ~50 kohm pull-up resistor at the PFI9 input.
Hope this helps,
Ed