Alright, I think I have it working. I'll post what I changed here.

I started looking at the php code for the theme and figuring out where things were rendered. In the theme.php there's a function themesidebox($title, $content) that seems to handle putting together the blocks (html, css etc).

$content seems to be in some cases a file name to the actual block php file and then the function opens it and incorporates it. But in my case for whatever reason the $content already contained the correct content (haven't figured out the logic in the main.php yet), but somehow even though $content contained HTML the file_exists method is still returning true, going through the process of loading a file and changing the $content to be the contents of a non-existent file.

No idea why the file_exists doesn't work properly in this function on my server...

So what I did is basically comment out that part that checks for a file name and it works fine.

Bizarre, but works for now.