[Amps] High SWR

[Ken-W9KB]

I was looking around on 15m this past weekend for that elusive multiplier during the Sweepstakes and I noticed my exciter was folding back power as a result of a high SWR between it and my amplifier. The SWR between amplifier and antenna was great (handled with Palstar AT-Auto Tuner – modified to accept two SO-239 inputs).
 
Since I was on a SteppIR at the time, I set my tuner to it's 'bypass' mode. I still had a high SWR between exciter and amplifier. Last night while playing around with it, I decided to add a low power tuner between my exciter and amp.. Bingo, full power out.
 
The Palstar AT-Auto Tuner disables the exciter's internal ATU function, do I have to add a 'tuned' the length of coax between exciter and amplifier or should my Alpha be happy?