Jim, when you get the low beep on the tuner it is out of the circuit.  the 
480 will tune anything under 6/1.  Yes it is more lossy than the internal 
tuner.
Now this is odd.
at 28.5 mhz with a dummy load, I get 54 watts out with the internal tuner, 
and 62 watts out with the internal tuner bypassed.  The power level is set 
at 100 watts.
On 1.805 I am getting 34 and 45 watts respectively.

I am suspecting insertion loss from the coax switch, will check that out and 
then start changing jumpers.
Any other ideas?
I have a 6 meter Motorola on the same power supply, turning it off didn't 
change a thing.