Actually, it is designed to  break the keying line  when a auto tune is 
  done.   The key line breaks, the radio drops power and goes to cw, 
then the tune is  done.   After the tune, the  key line  is enabled 
again, the radio returns to original power and mode settings.

Like you, I'm not sure I would trust  it with my life,  so as a rule I 
hit the switch to put the amp in standby for a tune.  But it is a nice 
emergency back up in case I forget.
It's like relying on the protection circuits in a SS amp to save your 
bacon all the time,  instead of being sure all is right with antenna, 
band, and swr.    This protection stuff may work a thousand times, but 
the thousand and first time, it may cost you a fortune.

73, Steve KW3Ah
On 1/16/2016 11:15 AM, John Miller wrote:
> I very heavily doubt it's anything more than emergency protection, not meant
> for tuning the antenna. Any amplifier manual will tell you put it in standby
> to tune the antenna, I'd even if it said you could, never trust a tuner to
> put it in stand by for you and especially not anything made by MFJ. that's
> jus not what it's made for, if I'm reading it right in the manual, it's SWR
> protection if the SWR is too high, not meant to tune the antenna with the
> amp running.
>
> -----Original Message-----
> From: Richard B. McDonald
> Sent: Saturday, January 16, 2016 10:48 AM
> To: [log in to unmask]
> Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> Hi John,
>
> Of course, I agree with this.  That said, reducing the radio's (TS-2000)
> power and placing the amp (1306) into "bypass" (not "standby") is precisely
> what the MFJ-998 is supposed to do when using its "Amp Enable In/Out" RCA
> jacks.  And, yet, it is not working.  Indeed, it is this automation
> functionality of both the 998 and 1306 for which I have spent a fair amount
> of money over and beyond what I would have paid for equipment that does not
> have such functionality.  And, this sort of automation provides an excellent
> backup if I make a mistake flipping switches, or forget altogether to do so.
> What's more, in my shack the 1306 is not within hands reach, so it is that
> much more inconvenient.  Hence, I am keen on getting this equipment to
> perform as advertised.
>
> 73,
> Richard KK6MRH
>
> -----Original Message-----
> From: For blind ham radio operators [mailto:[log in to unmask]]
> On Behalf Of John Miller
> Sent: Friday, January 15, 2016 6:13 PM
> To: [log in to unmask]
> Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> Any time I ever had an amplifier, I always tuned in the standby position,
> never with the amp ready to operate. I never had a solid state one but
> assume that's still an option, there is no reason to tune with high power,
> none at all.
>
> -----Original Message-----
> From: Tom Behler
> Sent: Friday, January 15, 2016 7:26 PM
> To: [log in to unmask]
> Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> To clarify my last post on the issue, I never tune with my ALS600  amplifier
> in the operate mode.
>
> I always tune with the amp in stand-by mode, just to be safe, and then, once
> the antenna is tuned, I put the amp in the operate mode.
>
> Sorry for any  confusion I might have created with my original reply.
>
> Tom Behler: KB8TYJ
>
>
> -----Original Message-----
> From: For blind ham radio operators [mailto:[log in to unmask]]
> On Behalf Of Tom Behler
> Sent: Friday, January 15, 2016 7:12 PM
> To: [log in to unmask]
> Subject: Re: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> Richard:
>
> It is probably because you are auto-tuning at a low output power level,
> which doesn't make the amp bypass mode a necessity.
>
> Perhaps I'm wrong, so I hope others will weigh in as well.
>
> Tom Behler: KB8TYJ
>
>
>
>
> -----Original Message-----
> From: For blind ham radio operators [mailto:[log in to unmask]]
> On Behalf Of Richard B. McDonald
> Sent: Friday, January 15, 2016 6:47 PM
> To: [log in to unmask]
> Subject: Ameritron ALS-1306 Not Going into Bypass Mode During Tuning
>
> Hi!
>
>
>
> With my Kenwood TS-2000, I use both an Ameritron ALS-1306 amp and an MFJ-998
> antenna tuner.  Both the 1306 and the 998 are connected to the TS-2000 with
> their respective interface cables.  I also have the 998's "Amp Enable
> In/OUT" RCA cables connected to the 1306.
>
>
>
> However, when I press the "Tune" (AT) button on the TS-2000, the 1306 does
> not go into bypass mode during the tuning process.  I cannot figure out why
> this is happening : (  I would appreciate any insights anyone has on this.
>
>
>
> 73,
>
> Richard KK6MRH
>