As Stirling has said - you haven't said how it all works. My M3 M4 M7 and M8 outputs from the computer all drive relays (driven by a Darlington array) They require an active low signal to drive them. I have noticed, in certain circumstances my Omron inverter says both M3 and M4 are on simulataneously (this is not allowed and the Omron flashes up a fault). This means that there is no output from the computer, i.e. the computer is at Ov. The relays and Darlington array are powered from the stepper driver board supply - via a 5v regulator, so if the computer is at 0v, both lines appear active to the Darlington and it turns both M3 and M4 relays on simultaneously. (It is probably turning on the M7 and M8 relays as well, but I haven't connected up my coolant yet )
The thing to do is check the signals from the computer, first at your breakoutboard board, and see if what is happening is being signalled by the computer, or if it is a mismatch of power supplies to your relay drivers. My breakout board is not powered, so it accurately reflects the output from the printer port. If yours is powered, you may want to disconnect the cable and try checking the port directly at the plug.
Some breakout boards have a disable pin as well, and if you have enble/disabled this from the computer, it may, when on E-stop, disable all outputs from the breakout board. This is fine, but if your relays are active low and powered from another source, this could be your problem.