Counting pulses in low power device
A circuit diagram of ALL the components involved is always a good idea.
If you have told us about ALL the components the diagram will be simple and easy.
However, OFTEN we find there is "stuff" not mentioned.

The term "comparator window" suggests hysteresis but this may not be what you mean.
Just moving the window is unlikely to be a vast help - except if the open circuit input is biased in some manner. The improvement due to lower pullup value MAY be due to harder 'pull' against the input signal (ie lower impedance vs input signal impedance) but this is not certain.  

'A LARGER hysteresis window should help - but will probably not fix the problem totally as an open circuit line MAY swing rail to rail. . 

Try adding "some" capacitance to the comparator input.
IF there is already capacitance there TELL US SO.

Try adding hysteresis to the comparator. (positive feedback)
IF there is already hysteresis there TELL US SO !!!!   

Show us a circuit !!!

Why not disable the circuit and/or short circuit the line when / while the sender is disconnected?