Threading not working on Mail 6.2 and 10.8. What to do?

I'd love to use threading mails. But the feature is extremely flakey for me. E.g. I see three mails with identical subject, sent on the same day next to each other in the same folder.
* I have Mail.app > Settings > View > View conversations: Include related messages (set to active)
* Mail.app > Menu > View > Organize by Thread (set to active)
This is very annoying, especially if you are an extensive mailing list addict and use many ticket systems. If then threading is not working - well your folders are a mess and you loose a lot of time trying to follow a single subject, scattered all over the place.
:S
Apple? Anything you can do, to improve this?

For Mail.
Do a backup.
Take notes of all account information or take screen shots. You may need to set the accounts up again. Quit Mail.
Copy the line below.
~/Library/Containers/com.apple.mail
Select Go/Go To Folder from the Finder menu bar. Paste the line into the window. You won’t see it.
Move the folder com.apple.mail to your desktop. You must move the entire folder, not just the contents.
Relaunch Mail and test. If the problem is solved, recreate any required Mail settings and import any emails you want to save from the folder on the desktop. If the problem remains, return the folder to where you got it replacing the one that is there.
Information learned from Linc Davis.
If you prefer to make your user library permanently visible, use the Terminal command found below.
Show User Library Directory in Mac OS X 10.7 Lion & 10.8 Mountain Lion
You might want to bookmark the command. I had to use it again after I installed 10.8.5. I have also been informed that if you drag the user library to Finder it will remain visible.

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