I'd eyeball the relays that power the auxilliary power and the fuses that supply them. FWIW, in my 02 2500 (old body style) there are two pink wires (pink and pink/white) that go hot in the run position (IIRC). There are two wires from the relay pack on the Viper that go hot in auto start for auxilliary circuits. If the monkeys who hooked the system up used just one of the Viper's supply wires to heat up both of the factory aux wires it could over-stress the Viper relay pack and cause it to fail. OR, if they hooked it up that way it could cause the fuse(s) on the supply (from 12v+ to the relay pack) to fail. I'd look at all the fuses on the vehicle AND the Viper system, including all wiring harnesses (which should be in a single location I imagine) for blown fuses. Then, if it's anything like my 791XV, it'll have a "relay pack" (basically a long, slender black "thingy" with about 8 or
10 heavy-gauge wires coming from it), and I'd look to it for damage.
Having the system run the engine but not actually blow the air (cold or hot, as you choose) into the cab is silly (that's half the reason for having remote start, I think), and since this isn't the first time this has happened to you I'd be wary of the installation. Closely checking the installation, and maybe finding the problem yourself will help you save time and money in the future, I would think.
Good luck. Let us know where that leaves you.
--HC
"I was having a bad day. A man said to me, 'Cheer up things could be worse!'. So, I cheered up and sure enough, things got worse." :)