Yeah, I would bypass the 31x to insure the phone lines/connections, etc are good. When the phone works 100% without anything else, put back the 31x and test that and when that is ok, plug the M1 back in and test again. Could be as simple as a loose wire - easy to have happen, but hard to find, and easy to fix.
This thing is driving me crazy. I unplugged the Elk from RJ31 and the phone started to work.
The teco seized LED on the left side of the controller came on and the keypad started to beep.
Inserting the cord back into RJ31 killed the phone.
I beleive that would be the telco alarm on the M1. It sensed the missing line. And that is making me think more and more about a bad rj jack... if the elk is working (sensing the line and next alarm is getting the trouble signals) then the phone line up to the rj is ok. it is the house wiring side that may be a problem.
A word on this, the DSL filter for phones is not going to do the job for security panels. At best you will communicate 80% of the time. just get a DSL filter for the alarm RJ31X. Of the few times I filtered the whole house with a regular filter I had to go back and install one at the panel.
You should be able to measure about 0 ohms with an ohmmeter from T to T1 and R to R1 with the RJ31X cord unplugged. If not, maybe a problem on the board or wiring to the RJ31X jack. With the RJ31X cord plugged in you should measure 50 to 60 volts DC on T to R and the same voltage on T1 to R1 terminals.