Hi there,
it seems to be an all time topic how to avoid those duplicate tickets which occur if one replies to a Cc thread out of the original RT scope. We are facing this scenario several times a day. This this should affect many users imho.
I started to use this Extension:RT::Interface:
:Filter::CheckMessageId.
This modified version (to work with RT5) of the original extension was first mentioned by @D3_cwhite in this topic: Searching ticket subjects
It’s working fine in general (no more duplicates) - there’s just one caveat I could not solve until now: We are using different Queues and Subject Tags, and the mentioned extension seems somehow only to refer to the configured value of $rtname, such it happens sometimes, that a second Subject Tag gets added to a reply. This concerns Queues where another Subject Tag is configured individually.
It does not break the overall function, but it does not look nice.
I would like to see such an Extension as part of the RT upstream. Really wondering why this did not happen until now. 
@JeramyMT Which Extension are you using? Can I find it somewhere?
@D3_cwhite Maybe you like to ask your colleague to also fix the above mentioned wrong subject tag insertion? 
Best
Matthias