This is a bit strange, and I have a feeling it is caused by something I did.
I had widget logic installed and working correctly. At some point in my theme development (and unfortunately I cannot confirm when) conditional widgets stopped showing up. It works if I delete any of the conditionals (and allow it to run on all pages) but as soon as I add something like, is_page() it will not show up at all. I did build a CPT and I am pretty sure that it worked before I added the Custom Post Type, but I can't for the life of me rationalize why that would cause it to break.