Hi Dave,
This is a bit confusing, I thought that the comparator outputs was on RA4 and RA5 respectively. Looking at the device overview in the datasheet confirms this.

However, in the PortC section, under PortC.1 and PortC.2, which I believe is where you looked, it says Capture input and Compare/PWM output for Comparator C1.This LOOKS like a typo to me and THINK what they really mean is Compare/PWM output for CCP1 which i think makes more sense.Is the comparator outputs multpiplexed between RA4/5 and RC1/2 and where do you select that?

I've tried to see what could cause the OP's problem but I've failed to find anything on PortC that needs disabling in order to function as digital inputs. Weak pullups crossed my mind but there are none on PortC so that can't be it.

/Henrik.