Re-install Mach. It's possible your XML are getting corrupted and it's not uncommon for a re-install to fix that.

Also is this a registered copy of Mach 3 or running in trial mode.? If it's one of the dodgy copy's from china then dump it a get the latest lock down version from Mach3 web site.
Check the version number and if it's a dodgy copy then I wouldn't be surprised if it's Mach2 or even Mach1.?

Ok I suspect the limits are tied to Enable signal of the individual drives but the Only way to fully know what's going on is to trace the wires back and see if they go to the drives or the BOB. It could also be a feature on the BOB but without knowing the BOB then can't say.
Turning the drives off using the enable signal is Ok has it keeps the drives powered up and holding torque applied to motors but really you want mach to know about it and stop the code running. This is easy enough to do by passing the same wire thru an input on the BOB then telling Mach to watch it.

If your not sure then post pics of control box has it may help.