Filtering of a 5 V square wave
"Here is the Max9926 system. This signal is Fed into CAMVR+. CAMVR- is left open circuit (floating). "


Don't leave the other side of the differential input floating, there's no path apart from the input leakage to charge/discharge the filtering caps. Tie the unused input to some reference near the middle of the input signal range with a resistive divider (you don't have access to the internal reference that the comparator is using).