May not be the problem, but I have suffered from this one...

When you home, it is possible that the axis barely moves away from the home/limit switch (and I am assuming that you have a single switch for home and limit). When homing, Mach3 treats the switch as a home switch so that it does not trip the "limit" function at this point. However, as soon as that axis has homed, it reverts to being a limit switch while Mach3 goes off to home the next axis. If the first axis is still just about at the switch trip point, it might actually trip the switch due to vibration, and Mach3 sees this as a "limit" event. The cure is to set the Mach3 parameters to move the first axis a couple of millimetres away from the point at which the switch tripped. I had this problem with proximity switches but I guess it might happen with mechanical switches as well. It's a quick thing to check - just a change of a few Mach3 parameters - so worth a try, perhaps.