I too have been having the same problem on a retrofit I'm doing. I set the ports and pins for the home switches in Mach3. Mach3 diagnostics show the switches trigger, but Mach sends the machine to the switch, ignores the change of switch state, and keeps going.
My setup is using a Galil DMC-1842, in Servo Reverse mode. Though I am not on-site at the retrofit to test on the machine there, I am suspecting that setting to be the culprit. The reason I say that is this: I brought the control computer back to my shop to test with. I hooked it up in stepper mode to test as I don't have any analog servos at the shop. I did a clean install of mach. Installed the plugin. Configured the plugin, setup my homes and limits (just exactly as I did on-site). It worked! At the moment, I suspect that Motor Type setting in the Plugin Config.
Also, I was told that I should set my limits and homes to identical values (i.e. - X Low Limit and X home are both enabled with the same port and pin configuration). I don't know if that was actually necessary, though. The next opportunity, I will try to determine that.
Shivu, be sure to let me know how you progress on this. This issue has cost me a lot of down time, as it may have you. I hope to resolve it soon.
Thanks,
Josh G.
P.S. - Let me clarify... My vertical axis (z) actually homes correctly, but the axes that home in their respective negative directions do not.