I've been puzzling over the symptoms you describe and I think I can explain what is causing some of your problems, but perhaps not all of them.
The CM-E1 is works in a manner like a 4-wire smoke detector. The EOL resistor is in series with the normally closed trouble relay and is in parallel with the normally open alarm relay in the CM-E1. This allows multiple detectors to be daisy chained together. In normal operation, the alarm relay would be open and the M1 would see the 2200 ohm EOL resistance, making the zone voltage about 6 volts or so. When the detector goes into alarm mode, the relay closes and shorts the EOL resistor, dropping the zone voltage to 0 Volts, and the M1 goes into alarm mode.
If the detector has a trouble condition, the trouble relay opens, creating an open on the zone loop, and the M1 zone voltage goes to 12V and the M1 senses the trouble condition.
When you specified the zone type of 0 (EOL/wireless), the M1 expects to see the 2200 ohm EOL resistance and about 6V on the zone during normal operation. When you removed the J2 jumper, I think you caused the CM-E1 alarm relay to be closed during normal operation, shorting out the EOL resistor. This should have caused an alarm condition at the M1, which is what you say you saw with the second CM-E1 that you installed.
What I can't explain is why this didn't also happen with the first CM-E1. I think you say removing the jumper made it work. I'm not sure how that could be, unless you have some high resistance in your loop wiring. I would measure the voltage at the M1 terminals on this zone and see what it is when the jumper is removed. That should give us a clue to what is going on.
I think the proper zone def and type for these zones is Zone Def 17 (CO 24 Hour) and Zone Type 5 (Fire, 4-Wire Smoke Detector).
You should install jumper J2 on both detectors.