The preamp output is a simple non-amplified circuit. You get no amplification to run speakers from these channels unless you first run the signal to an external amp. If you do get any appreciable volume it would be at full blast and barely audible. So running a preamp out to an external amp while running the internal amplified channels to speakers really is a negligible load on the HU unless the preamp signal is split multiple times or you do something wonky with the wiring causing an out of phase issue, an open ground situation, or you incorrectly ohm load the any of the channels.
It does sound like the HU is letting out all the magic smoke and is failing. Most likey its the mosfets. Some of these units were built using a cheap tin based solder and as the circuits go through hundreds of heating and cooling cycles the solder will develop micro fractures eventually leading to an open circuit.
The way the channels will appear to phase in an out is, as one portion of the HU heats up it will cause the cracked solder to expand and as the circuit gradually closes you get a crackling sound and then a solid signal through out the unit.
If you are feeling froggy you can open it up and with a soldering iron go over all of the solder points. But be warned, there are tons and its time consuming and there is no guarantee that it will fix it either. Given enough time, partial voltages, low current situations... it could just be damaged beyond repair.
Edit: One thing you wanna check before tossing in another HU is, as I mentioned before, correctly Ohm loading the channels. If you use a 4Ohm speaker on an 8Ohm channel you will eventually fry that channel. If you use a 16Ohm speaker on an 8Ohm channel you will be fine. The issue comes with a simple lesson in electrical loads. Voltage (V)=Current (I)X Resistance(R) where voltage is measured in volts, current is measured in amps and resistance is measured in Ohms.
To be simple you can use 12v, cause its what cars use, and use the following rule of thumb. For voltage to remain constant current is inversely proportional to resistance. So to maintain 12v at 8Ohms your current must be 12v = I x 8ohms, so we solve for current, I = 12v/8Ohms = 1.5amps. So if this is how your HU operates and if you use a 4ohm loaded speaker 12v/4ohms = 3A. You double the amount of current when you decrease the load. In all circuits current is what produces heat. God forbid you use a 2Ohm speaker on a HU rated for 8Ohms, you'd be pulling 6A and would overheat the unit very fast on that channel.
