Mail is linking unrelated emails into conversation threads - is there a fix for this?

Mail is putting unrelated email messages into conversation threads. This is making it hard for me to find emails relating to different projects. The emails don't have anything in common apart from being addressed to me - different senders, subject lines, no content in common. I like working with conversations, but this is a pain.
I've seen several discussions online about this issue going back some years, so it's a real shame Apple haven't found a fix for this. I've read a couple of recent discussions here that link this issue to Yosemite - however I'm not using Yosemite (it's a work computer and they are slow to allow us to upgrade). My details are as follows:
MacBook Pro (13-inch, Mid 2012)
OS Mountain Lion 10.8.5
Mail v6.6
I know how to switch off 'Organize by conversations' in the View menu, but that isn't fixing the problem, it's taking away functionality that I like. I have tried unchecking 'Include related messages' in Preferences, but that doesn't change anything. I've tried rebuilding the Mailbox, nothing changed.
One thing that I hope Apple developers take note of - there doesn't seem to be a way to manually disassociate individual email messages from threads. That function would be really useful.
Anyone got any ideas?
GM

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.
Reindex messages       Mountain Lion
Send Apple feedback. They won't answer, but at least will know there is a problem. If enough people send feedback, it may get the problem solved sooner.
Mail Feedback

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