Thanks for the info. I did some testing and found that the themes work differently for some reason... here's the specifics.
First I chaged the query in the popularbox.php file to match that of the featuredbox.php file so I could still use the dynamic info, but oddities occured. As you can see in the pictures, it loads everything as expected (both boxes update) in the 'Default' and the 'Dark' themes, but fails to update the box in the 'Crazy' or 'Purple' themes as well as my own theme based off 'Crazy'. It would also show the changes in the CMS no matter what theme was loaded.
I went back and changed the query back to default and tried all the themes, but the box would not update properly at all in any theme and in the CMS ie: still shows default information.
I'm going to have a go at just editing and hardcoding the box next. I do still have a local testing copy loaded for any fixes or suggestions though.