Problem with large email imports to Mac Mail

So I am trying to transfer a large archive of emails (probably about 50k emails in total, in folders of 1-10k or so each) from Thunderbird to Mail, and it hasn't been easy. It's terribly slow, so I've started to do individual mailbox transfers one by one.
The problem I'm having is that once large mailboxes are transferred over, Mail crunches many of the messages in those mailboxes into a single thread. For instance, one folder with a total of 5k messages appears after importing as a folder with 2500 or so individual messages, and 2300 messages all glued together as a single thread. That's not ideal, but what's worse is that this same thread seems to not be getting stitched together with messages arriving in my inbox, generating complete confusion. I tried just deleting this monster thread in order to just selectively import some messages using my IMAP server, but the thread actually won't delete at all (it disappears briefly, then reappears once I navigate back to that mailbox).
Really want to use Mail, but finding this process quite frustrating.
I'm working from a new iMac with Yosemite, Mail 8.0.

Hi, not certain what the problem is & not on 10.10 right now, but check Mail's menu, something like View & look for something like not display as threaded.

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