The email notifications from the forum (seems to be Jive/ClearSpace) have a unique postfix on the subject lines which prevents gmail from using its nice threaded conversation UI stuff (though I guess helps Jive/ClearSpace figure out threaded replies).
I wonder has anyone figured out a way of using gmail with the email notifications so that things are nicely threaded? I guess using emails as a ping and the forum UI is still probably best 
AFAIK, it's not fixable with this forum engine. We are considering moving to another one.
I made the same observation last week (oddly enough, I can't find my post any more, maybe it was removed because it was off-topic), and the answer was that they would look into it.
I’m kind of baffled why a forum would think it’s a good idea to add a unique string in each subject of the emails, or worse, not even make that configurable.
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Cédric