I too have the Viper system (5701) and the rear doors really don't apply much. I doubt it's an installation error because they have done a good job. Everything functions.
I had them activate the passive arming so when I leave my vehicle and close my doors (and all other doors are shut), it will take 30 seconds for the viper system to arm itself then 10 seconds after that for the doors to lock automatically.
The thing is though, with the auto locking it doesn't care if the rear doors are opened or closed. As long as the driver, passengers and trunk are closed, the viper will arm and lock regardless of the rear doors.
So for example; if I get home, turn off the Envoy, get out and shut my driver door the countdown begins. When I open the rear door to get some thing out, it still will eventually arm and lock. When it does and I shut the door, no alarm goes off.
I guess Viper didn't think it through about the rear doors or maybe we're suppose to buy something extra.