Hey Brian;
I found the manual online - we're talking about the FM-870, right?
http://www.commandocaralarms.com/man...870install.pdf
Anyway... the wires I'd start looking at would be:
H5/1 - White/Black, Negative safety shutdown
H5/2 - White/Violet, Positive safety shutdown
H5/3 - Black/White, Remote start enable (this is the one I was thinking about above)
H6 - This is the door look trigger
You may also want to reset the alarm options back to factory. This is on Page 22, "Return to factory default setting". That would clear up any chance that it's in some weird "safety" mode.