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.
"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." :)