I had an index.html living next to index.php at the root of my wordpress installation. When going to my domain it was loading the index.html which is what I wanted.
I then went to work making some tweaks to my WordPress settings. Everything was fine until I was messing with the Widgets. As I made changes to some of the widgets it was clear that it was trying to access mydomain.com/index.php but that was being redirected to mydomain.com/ which was causing the index.html file to load. This raised hell with the widgets page and the Total Widget Control plugin.
I wasn't able to save any changes to the widgets and had to remove the index.html file in order to make WordPress work correctly. All of the widgets that I had previously loaded were lost.
It appears this changeset #9203 is what changes the url.
Its possible that this could be a bug with Total Widget Control but this issue caused me to lose several hours of work.