Hi,
I have the same issue with Yosemite's Mail.
When freshly starting up Mail, the Flags are shown in their colorful icons.
Then, leaving Mail open, the Flag icons turn into text for the color name. Very weird.
At one instance, I saw a few older email with the colored Flag icons, but the new emails were in text. I should have taken a screen shot.
In any case, it does seem to change from colored Flag icons, to flag color name text over time.
Restarting the Mail app will restore the Flag icons once again, but then again over time, they will change to text again.
No other functional problems with Mail app. It's just 'ugly' looking with no Flag icons, but just text in the Flag column.
NO 3rd party plug-ins installed. Latest Yosemite 10.10.1 with Mail version 8.1 (1993).
Any fix advice would be appreciated.
Thanks in advance!