so my cnc runs mach3 and it uses the pmdx-126 board.

I have a tormach passive probe, which when hard wired in works perfectly from j15 and gnd on the pmdx.

ive had a very helpful chap made an IR sender and receive for me in an attempt to turn the wired probe into a wireless probe, but were having problems with mach3 and the IR receiver working correctly.

when the probe is hard wired in, all you do is shorty j15 to gnd

we are now switching 5v on and off

are there settings in mach3 I can adjust to get my setup to work?

There may be a setting on the PMDX board, check the manual.