Random E-stop and limit alarms -Software or relay board related?

Last winter I started conversion of an older mill/drill to a 3 axis stepper driven CNC. I got the mechanicals done, ballscrews, motors mounted etc. then covered it up and went on with my regular work. A couple of weeks ago I downloaded the Mach3 trial software and started building the control using Gecko 203Vs, an older Hubbard CNC (Ebay) breakout board, a Hubbard Limit switch board, Kelling 70VDC power supply, and the usual bells and whistles.

Once I got it all wired and powered up I started having random E-stop and limit switch errors pop up in Mach3, requiring a reset. Usually it happens when nothing is moving at all. Occasionally I will see a quick flash on the pin designators on the diagnostics page just before the e-stop alarm starts again (when nothing is moving). I have been in touch with Brent Hubbard and he very graciously sent me a new generation relay board even exchange for the one I purchased last year. The new model appears to have been designed with mach3 and gecko drives in mind as both are mentioned in the set-up instructions. I installed it this morning and the problem with the estop errors has slowed down to once every couple of minutes with nothing moving but has not completely gone away.

I am running 4.3A NEMA42 625 oz/in motors on X&Y and a 4A NEMA34 465oz/in motor on Z. I am wondering if I have somthing set incorrectly in Mach3 where there is some kind of feedback occuring which causes the estop/limit alarm to kick in. I have jogged the axis many times and the problem usually occurs during motor start-up or slowing while moving, but sometimes the alarm goes off whrn nothing is moving at all.

Is there some setting in Mach3 that I could have set wrong?

Thanks in advance -Mike