The voltages are correct (not too high) for the system.

The blower motor amperage draw (not volatge) could cause the resistors to 'smoke'.

Did all this start right after you did the remote start process?

Perhaps you could just leave the heater fan switch on '4' (which bypasses the resistor...) for remote starts.

Well I've been using my remote start for about 2 years now, so that's not anything new .. but it could be that some of the wiring is coming loose and causing stuff to go haywire (which I kind of doubt because the blower resistor is the only electrical part being affected).

What happens is that I start my car with my remote, and it usually runs for about 2-3 minutes to warm up. Then when I get inside I notice that my controls don't work and there's a funky burning smell coming out the vents. Then that's it ... it doesn't work after that.