RE: Auto reply not working
The user having the same email address as the Queue is actually just due to business expansion i guess, what was once a generic support@ manned by one person, turned into multiple people using the one inbox (should have been converted to a shared mailbox), then the CRM was finally introduced... long story short you actually pointed me in the right direction!
After looking further into the duplicated mailboxes I performed the following steps,
1) Removed the Queue and associated Mailbox.
2) Checked incoming mail was been correctly assigned to the mentioned User as email activities
3) Recreated the Queue and assigned the same email address
Then i was back to the same problem of emails not been assigned to either the user or queue... but after reading the below link i realized that the global mail setting for "Set To, cc, bcc fields as unresolved values if multiple matches are found in Incoming Emails." was set to yes, after changing this to no, mail flowed through to the queue, cases created and automated mail was sent.
That said it does show email activities now belonging to both User / Queue, I can live with that as it can't really be avoided due to initial design decisions
https://support.microsoft.com/en-au/help/4339830/an-email-fails-to-be-created-in-dynamics-365-with-a-norecipientmatch-s
I guess i just needed someone to bounce ideas off, thanks for your time Paul much appreciated.