If I understand your circuit correctly, you have a resistor to Vcc that you can either connect or not connect to a pin through a jumper - correct? This would mean that if the jumper was in place, it would pull the pin to Vcc, and if the jumper was not installed, the pin would be disconnected.
If this is the case, you will have trouble reading the state, since an unconnected input pin's voltage state is indeterminate (NOT low). You would be better off connecting the pin directly to GND or Vcc through the resistor, and then use the jumper to connect it to the opposite supply. If you are connected to port B, you could enable weak pull-ups and connect the pin
directly to GND through the jumper.

If your circuit is wired as I think it is, you may have to use a technique that I call a "slam-read": That is, make the pin an output and drive it low. Change it immediately to an input and wait one processor cycle (using the
line "@ nop") then read it. If their is nothing connected to the pin, it will be low on that read (stray capacitiance will keep it low for awhile after the WRITE). If it has a resistor connected and pulling it up, it will be high on that read (since now the resistor will have charged up the stray pin capacitance).