You said Mach3 is what E-stops your mill, so Mach must be picking up a problem somewhere. I would look over the Limit/homing switches real good. WIggle the wiring around, tap on the switchs, work the switch control arm/button and see if one of them is on the very edge of triggering or loosing connection. A lot depends on how the switches are run and if they are in series ( which is a good way to have them wired) then all it takes is a break in the curcuit anywhwere to trigger Mach.
It doesnt sound like you have the spindle hooked to mach, but do the same checking with all the drives and there wiring. If you cant find anything then unhook each drive one at a time ( with everything turned off ofcourse). So you would unhook one drive and motor, turn mill on and let it set and see if it E-stops. If it still does then hook that driver and motor back up and try the next one.
Somewhere Mach is picking up a problem. Try to eleminate eacg curcuit one at a time until you track it down. Limit/homing switchs are the worst for having problems so start with them.
Now i havnt worked with Mach or CNC for a while, there may be some problems others are having so keep up with your post incase someone knows of such going on.