Yes my Estop also stopped the router but this is not right. Mach3 controls the cnc and when Mach3 is not loaded nothing should run on the cnc.
I think you are wrong here personally - if mach is not loaded it should not be possible to engage the safety system so that the tool rotates - very unsafe.
Also, on a pc, if Mach is not loaded and controlling the LPT port, anything can happen at any time, its a dangerous situation having machines hanging off an uncontrolled port on a pc - the safe setup would be to boot pc, load Mach3, power up the BOB, power up the controlled machine, take Mach3 out of reset into the run condition.
When a PC is booting, the ports get polled and that can do very odd (and dangerous) things, my plasma torch has been known to fire for a second if the system is not started correctly.