Chuck,
I think what you're describing is normal behavior of the "Multi-Horn" function. On many of these RailSounds 3 pieces, a simple horn push while the unit is at rest will result in a somewhat muted, dull horn sound. The same horn press, while the loco is moving, will result in a much more "dominant" horn sound.
If you don't think that describes what you're hearing, I'd say to check the unit's speaker. I can't think of anything electrical with the RS3 audio and power boards that would cause the selective sound problems you're describing.
TRW