When I power up Mach4, it gives me an EStop  error saying X-- Limit is triggered.  (In the log file it also says the Y-- is also triggered.  None of the physical switches are closed - the gantry is in the middle of the table.  When I go to Mach4's Configure Menu and choose Mach the pop up dialog with tabs appear.  If I close this  tab, the error clears even though I haven't changed anything in any of the tabs. 
My Home and Limit switches are the same.  I've changed it to where I only have X and Y Home and a X+ and Y+ Limit and X Home and Y Home, and I still get the error on the X+ and Y+, so I don't think it's a case of confusion of where the Home and Limit inputs are the same switch.
The problem seems to a case where on start up Mach4 isn't fully 'reading' the setup in the Input's tab, since when I open the tab and close it in the log file all of the switches are configured to "low" and the problem clears itself.
I've attached a log file showing the change as well as the profile.