First off, functional information on the machine.
ESS Smoothstepper
C11G for controls
DMM Servos and drivers
2 motors driving y axis gantry, single motor running x axis and another running z.

So here's the issue, I need more inputs so I got a C25S board. I changed the port the C11G was plugged into from port1 of the ESS board to port3. I then changed the pinout and all details in Mach4 to reflect the change of port.
Here's where it gets a bit odd, the slave motor on the y axis starts moving just a brief pace behind the master when moving the y axis, bad enough that it faults out the drivers on occasion.

I've set things back as they were and reloaded my backup from before I made any changes. All back to normal now.
Any ideas on what to look at that I may have missed?

That's very odd...
I would try making a new profile from scratch, it doesn't seem like the profile would have any bearing but getting the .ini rebuilt fresh solves some pretty abnormal conditions for me quite often.
If that doesn't work I can try to replicate it here.

A reasonable solution

I'll give it a shot then, thanks.