I added C30,31,40 and 41 to rung 7 befor the jump to stage 2 and didn't fix the problem.
Rung 6 loads the homing file for all axis, rung 7 jumps to stage 2 and homes Y axis, jumps to stage 3 and homes X and Z, then jumps back to stage 1. This process works fine. Rung 8 loads the Jog X file. This also works fine (I can jog X left and right in stage 4, then jump back to stage 1. Rung 9 and 10 should load Jog Z and Jog Y file into CTRIO 0 and CTRIO 1 respectively. This is where my problem is. Nothing happens. Any other suggestions?