You need to either pull the pin high with the resistor (or use internal pull-up,if available) and then short it GND with the jumper OR pull it low with the resistor and short it high with the jumper. The way you have it now leaves the pin floating when the jumper is not in place which makes it highly unreliable.

As for the code, your first version should be fine but I'm not sure if NOT is a valid operator in PBP.
Code:
If Jumper THEN
If Jumper = 1 THEN
If Jumper = 0 THEN
If ~Jumper THEN   '<---I think this is valid for "not"  ...
/Henrik.