Okay, here's what I'm getting:

Doorbox works on another system.
No doorbox works on this system.
This system works correctly if the doorbox is simulated.

I'm thinking that the problem pretty much has to be wiring. Either the doorboxes are not being wired up correctly on installation (or the box they're going into shorts the wiring screws to ground, or something like that), OR the wire run is too far from the system.

Take the doorbox to the MDF and wire it up there. If it works, there's a problem in the wire run. If it doesn't, then it's programming.

Could also be a port going bad on the system, but that's a dark horse.