Apple Mail in Yosemite not downloading complete messages

My Set Up:
- Early 2011 MacBook Pro 15 inch.
- Yosemite 10.10.1
Since I upgraded to Yosemite, my Apple Mail is not downloading email content. I have to manually click on each message header to download the content of that email. See the screenshots below.
This screenshot shows how the message appears in the Inbox when it comes first.
And if I don't do anything it will stay as is. And the below image shows the message with its downloaded body after I select the empty message.
How can I make the message download automatically (the way it was before I upgraded to Yosemite)? Not having my message download messes up with other Smart Mailboxes.
Any help is appreciated.

Ok. Thanks.
I archived maximum email from my account and left around 300 messages in my Inbox + Sent Items.
Then I Rebuilt the account. I saw in the lower left corner the Mail Activity status where it started downloading the messages.
In parallel I had the Activity Monitor open to check the CPU usage. It was around 30%.
It took around 5 to 10 mins to download those 300 messages. But on my mail app only some of the messages were completely downloaded while rest only showed the header and no body. I left it that way.
The Mail Activity is done with its job. The status bar is gone. But the Activity Monitor still shows Mail app at similar CPU utilization levels (around 30%).
The issue is that my Mail App does not show any additional messages downloading with their bodies. Its almost like it is stuck at message number X.
While the CPU is still showing 30% utilization by mail, I have switched the UI to NOT show any conversations. This way every message is visible in the list. I have put the mac on Caffeine for next 5 hours so that it does not sleep.
Will update the thread tomorrow.
Thanks for your help.

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