The bias may be off on the 2 channel amp as these amps do run warm. The higher bias ones should sound a little better so you could use the 3 channel to run the front 3 speakers.
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If anything the Balanced should run warmer only because there would be more gain but that is only if you didn't calibrate the Pre-Pro and gad everything set to the same volume. If it is calibrated then it should not make any difference at all.
What I mean by bias is that all class AB and A amps have a bias to aply voltage to the outputs so that at low listening levels the amp sounds better. If you put your hand on the heat sinks they should all feel the same temperature. If they don't, then the amp should be re-biased for better sound. If they feel the same then the difference is only because you have 3 channels in one and 2 in the ither so the 3 channel will produce 33% more heat overall.
Oh this is a bit embarrassing: I leave the AMP-3 on all of the time and the AMP-2 was being triggered from my Proceed PRE. This accounted for some of the temperature difference. I've now had both amps on for the past 48 hours and there is still a difference between them - the 3 is almost too hot to keep your hand on it, but the 2 is "just warm". I'll experiment to see if there is any sound difference when driving the fronts with the hot amp-3.
Thanks again Duane.