Partially solved! i.e. I think I know what is wrong, but not why it happened to 
this particular App.
Short answer: Gnucash is in quarantine due to a Mac OS feature called 
Gatekeeper Path Randomization (GPR). Running the following command in a 
Terminal window removes the quarantine flag
xattr -dr com.apple.quarantine /Applications/Gnucash.app/
After this command, placing Gnucash in the Dock from the application folder no 
longer results in a duplicate icon and app behaviour is normal.

Now, why Gnucash got quarantined in the first place is what I need to work out. 
It shouldn't happen if an application is copied from the .dmg file to the 
Applications folder.
I am currently chaining through the following link where someone was 
experiencing similar behaviour with an app called Blender. The link pointed me 
in the right direction for a solution
https://developer.blender.org/T49473

I'll report any further findings here if I think it is an issue caused in any 
way with how the Gnucash .dmg file is built, in case it impacts devs. Now to 
get to the bottom of GPR on the mac.
Thanks for all your replies/suggestions
Glen

On 14/06/2018, 21:49, "gnucash-user on behalf of Adrien Monteleone" 
<[email protected] on behalf of 
[email protected]> wrote:

    On this note,
    
    Are you installing to “/Applications” or “/Users/your-user/Applications”? 
Either should be fine, but if you do have some corruption in your user profile, 
installing to /Applications might help.
    
    Regards,
    Adrien
    
    > On Jun 14, 2018, at 2:28 PM, Adrien Monteleone 
<[email protected]> wrote:
    > 
    > Try creating another user account on the Mac. Add GnuCash to dock and see 
if the problem persists. It might be an issue with prefs files for your user 
account. If you don’t want to go that route, or in conjunction with doing so, 
when the question mark appears, try either Force Quitting (technically 
relaunching) Finder from the apple menu, and/or execute a “killall Dock” 
command from a terminal. That might give you the reset needed. Also, keep 
Console.app running and check it when the question mark appears to see if there 
are any related entries.
    > 
    > Regards,
    > Adrien
    > 
    >> On Jun 14, 2018, at 2:15 PM, Glen Byram (Gmail) <[email protected]> 
wrote:
    >> 
    >> Yes, it certainly is annoying. As we speak, Gnucash has just got its 
grey question mark. The machine has been woken up for about the 10th time since 
I last did "Keep in Dock". No full restart in that time (I rarely do with the 
mac). No issue at all the previous 9 or so "wake-ups. I am starting to think 
that something is wrong with this specific Mac. I would definitely think that 
was the case if other apps had the same issue, but they all work fine.
    >> Regards
    >> Glen
    >> 
    >> 
    >> On 14/06/2018, 15:07, "gnucash-user on behalf of Adrien Monteleone" 
<[email protected] on behalf of 
[email protected]> wrote:
    >> 
    >>   I don’t think a second executable is the issue. I frequently see this 
problem with Firefox. Occasionally after it updates and re-launches, it will 
drop a new icon on the far right of my dock for that updated instance. I just 
close it and relaunch it as normal with the original icon. (which uses the 
updated instance, there is no older executable anywhere, even if I clicked that 
original icon while the other was still open.)
    >> 
    >>   I don’t have even a guess as to why this is happening though once 
GnuCash’s launcher is stored in the dock via right-click and ’keep in dock.’
    >> 
    >>   Regards,
    >>   Adrien
    >> 
    >>> On Jun 13, 2018, at 6:56 AM, David T. via gnucash-user 
<[email protected]> wrote:
    >>> 
    >>> My dock works, and has worked for a decade. Perhaps you are using 
GnuCash from two places: Applications, and the dmg? I say this because the “?” 
could happen after restart if the dock item were linked to a dmg file, and the 
dmg weren’t reloaded on restart. 
    >>> 
    >>> Similarly, a second dock item would suggest a second executable in a 
different location—although how the dock item could reference a different 
executable is beyond me. 
    >>> 
    >>> David T.
    >>> 
    >>>> On Jun 13, 2018, at 5:56 AM, Glen Byram via gnucash-user 
<[email protected]> wrote:
    >>>> 
    >>>> I am running macOS Sierra 10.12.6
    >>>> 
    >>>> I cannot get Gnucash to reside in the mac dock like other apps. I may 
have reported this issue before but I can’t find anything in gnucash-user and 
whatever solution I thought I had was only temporary.
    >>>> 
    >>>> 
    >>>> 
    >>>> 1)  The normal process for placing an app into the dock permanently is 
to just drag it from the place it is installed (usually the Applications 
folder) to a position on the dock that you want.
    >>>> 
    >>>> Once this is done, you should be able to launch the app from the 
resulting dock icon. The same icon should bounce as it launches, then stop with 
a dot under the icon to show it is active.
    >>>> 
    >>>> The behaviour I see is that a duplicate Gnucash icon appears at the 
end of the dock and it is this one that bounces/indicates active app. Although 
functionally OK, I don’t want 2 icons for the same app when its running one 
instance.
    >>>> 
    >>>> 
    >>>> 
    >>>> 2) I have tried the alternate method of keeping Gnucash in the dock; 
Make sure there are no Gnucash dock icons then launch it directly from the 
Applications folder. Once launched, right click on the active dock icon and 
select Options->Keep in dock. After that, I can move the icon to the position 
in the dock I want it to be. It now appears to work perfectly. Unfortunately, 
after I log out, or after some periods of sleep (not sure on the number-seems 
random) the Gnucash icon gets overlayed with a question mark indicating that 
the location of the app is now unknown – even though it has not changed and is 
still in the Applications folder. If I restart the machine when the Gnucash 
icon is working as expected, I get a grey question mark in the dock without 
even the Gnucash icon. Mousing over the grey question mark gives a Gnucash 
tooltip but of course it won’t launch as the location of Gnucash is unknown. 
The only option is to right click on the icon+question mark or question mark 
(by itself) and select Options->Remove from Dock.
    >>>> 
    >>>> 
    >>>> 
    >>>> As far as I can tell Gnucash is the only App I have that exhibits this 
behaviour. At the start, I thought I had fixed it using method 2 above. Then 
after several days the dreaded question mark appeared over the icon.
    >>>> 
    >>>> Other things I have tried include making an Alias for Gnucash and 
dragging that to the dock. It didn’t work and behaved like 1) above (duplicate 
app icon on launch).
    >>>> 
    >>>> I decided maybe the dock was corrupt so I did a reset to default: 
Terminal command; “defaults delete com.apple.dock; killall Dock”
    >>>> 
    >>>> This meant I had to rebuild my preferred dock from scratch. There was 
no difference. All other app icons behaved as expected apart from Gnucash.
    >>>> 
    >>>> 
    >>>> 
    >>>> My conclusion is that Gnucash must have a launch process different to 
other apps and/or the drag/drop to dock processing must be different.
    >>>> 
    >>>> For the time being I tend to stick to Option 2 above as I prefer a 
single launch icon on the dock. When Gnucash eventually gets it’s inevitable 
question mark I remove it from dock then re-instate it as per 2) above. But it 
would be nice to have no need to do that. It’s not urgent or a matter of life 
and death but something to ponder.
    >>>> 
    >>>> 
    >>>> 
    >>>> Cheers
    >>>> 
    >>>> Glen
    >>>> 
    >>>> 
    >>>> 
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