cannot get the s4 to run a dual course on the split secound program in program 1 or 3 is this a software issue or does the s 4 only work the computer in program 3

The S4 only communicates to the PC in program 3.

The default input mapping is:

Red/Yellow start = Channel A / "0" banana plugs
finish = Channel A/ din plug photocell/ Input channel 1
Blue/Green start = Channel B/ "3" banana plugs
finish = Channel B/ din plug photocell/ Input channel 4