I read somewhere that I need to have the site with the mu install set as the main domain for my account so I went ahead and did that. I am guessing it will work fine now with the mapping plugin so I will just go ahead and mark this as resolved.
My example url’s may not remain valid as I am trying new things and new installs but the problem still stands.
I am familiar with this but only because I have purchased themes from themeforest. Are you working with a premium theme? Some of the theme authors have put safeguards in areas of the themes to combat people snagging and nulling their themes. You may want to talk to them if you purchased the theme as that is likely where it is coming from.
If you are not, I have no idea. I have never experienced that with a normal wordpress installation.