I am currently experiencing issue's with homing, the x and y axis move different amounts each time ref all is pressed and mach say they are homed and reset the DRO to the set figure but are clearly not, and the LED is not lit in the diag screen, the same with the z homing but this moves very small amounts, as little as 0.2mm every time the ref home button is pressed, it resets the DRO but no LED is lit either in diag, if I manually jog all axis to the switches the LED then lights up. Recently I have replaced my old BOB with a new one and also replaced the stepper drivers and installed a new 36v psu to power the drivers, the homing switches used to work before installing the new hardware, thinking it would be sufficient I have used 2 core plastic coated cable for the step/dir signals from the BOB also the same type of cable for the power from the psu to the drivers and orange 3 core cable (like you get from a lawn mower) for the main power to the psu, the cabling from the driver/vfd to the motors is the original wiring in the machine. I have read previous posts on noise and cable screening, would it be highly likely that this is a noise issue coming from the lack of screened cable in my setup?

This is how my conversion looks - some advice greatly appreciated

First give your debounce interval a try, start at say 500 and see if that helps if it does you have noise issue's .
Also you may have a corrupted xml file . if all else fails write down all your settings and uninstall MACH and reinstall it re-enter you settings and see what you get.

I have had to do this before and i know it is a pain in the butt, but it very well could fix it ,there are some bug's in mach that crop up now and again only the CNC god's know why !

would it be highly likely that this is a noise issue coming from the lack of screened cable in my setup?

Yes you have a noise issue and with low voltage signalling everything is best shielded and properly grounded.
Regarding you mentioning the LEDs not being seen on Diags page. You will be unlikely to see that due to the refresh rate of the screen but the Mach driver is very fast and will see noise as signals.
 You may get away with setting a Debounce Interval as woffler suggest, possibly even have to try higher but really the best option is prevention rather than cure so shielding is the best way to go IMO.

Hood

Should the Index Debounce be adjusted too or just the Debounce Interval?

just the debounce interval

Adjusted the debounce figure to 2000 and the homing switches now work ok. Thank you all for your help. I will look at changing the cabling to screened, but for now it seems to be ok.