if you do not have continuity between 4 and 6, see if you get continuity between 4 and 5 or between 5 and 6 each time you press the switch. if so, the middle row of your footswitch seems to be working.
now test the 1-2-3 and 7-8-9 by seeing if you are getting continuity between 1 and 3, and 7 and 9? (I think that is the same as what you were testing on the PCB)
you can isolate whether the continuity between the red dots, and between the green dots is due to the switch by removing one on the wires from the footswitch for each color and seeing if you still get continuity between the reds and the greens on the pcb, OR see whether you still have continuity between 1 and 3, and 7 and 9 after one wire is removed at the switch from each set.
so -- is the continuity coming from the footswitch or from the PCB?