Mail thread in Apple mail not working after updating to Yosemite

I just upgraded to Yosemite a couple of days ago and I noticed that my mail threads are not working properly. Instead of having threads categorized by the subject line, I have thousands of emails in just ONE thread that are completely irrelevant to each other. I have deleted my email accounts completely and reinstalled them from scratch and they still have the same problem after my emails are dowloaded from my IMAP server. I have also tried to rebuild the email account and the same problem happens. I get around 700 - 800 emails a day so the thread function is extremely crucial for me to be able to track all of my emails, but there is no way to do it now when everything is bunched together.
Anyone else running into the same issue? I am using a third party host (Bluehost) as my hosting service, but this problem never came up on the previous operating systems or my IPHONE. Those still work just fine.
Thanks
S

The longest thread about this seems to be this one: LINK
Best course of action now is to describe the problem to apple in the feedback form: LINK

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