I'm pretty sure that at least one of the Phase 1 inputs is active low (0V on the input), possibly the one called EFO or EFK.
If whatever is holding that high (+24VDC) is not reliably doing that, and the software senses it is low (i.e. active) then the car will go onto Phase 1.
This could be a problem with wiring (perhaps an intermittent connection), momentary voltage dips (check power supply feeding this input's Remote Station), or loss of communication to the Remote Station (check it's not a flakey IDC style connector, run an RSL test and look at parity errors, etc.). If you are able to set up a camera watching the service tool screen (M-1-1-2 ?) where EFO, EFK and other fire-related inputs are shown, you might be lucky enough to see something glitching.
