Even though you might not have provided very much of an answer…but somehow your comment lead me down the right path and I figured it out.
The CSS was not corrupted…
The theme uses dynamic PHP (muffin builder) to make changes to the CSS.
The CSS files are not static.
Your plugin creates static .css files and when I turned off the plugin the cached changes were not being loaded.
So I followed similar steps listed above…but I also re-updated the theme and wordpress (keeping the cache clear and the plugin off) and all of the settings went back to normal.
You were right….it was an INSANE problem. Hell I could barely figure out how to explain the problem!
Thanks again Emre – great plugin by the way!