Sean, It sounds like Brandon has given you the necessary things to try for this particular issue. So I want to be sure we are not missing something. When he suggested to look in the AutoSave folder, I want to be sure we were actually looking in the correct directory.
C:\programdata is a hidden folder on most systems. So if you were actually looking in ProgramFiles, you would not have found the AutoSave folder. If you do not see the ProgramData folder when you look in the C drive, paste the path that Brandon provided into the File Explorer window.
If you were looking in the correct location, there is one more thing we can try. If this fails we will need to remote into the system so we can dig a little deeper.
You should see the attached .reg file. Download this file and double click it. Agree to the couple of dialog windows and it will clear out the V6 registry. Keep in mind, it will set MediaShout back to factory defaults, but it will NOT delete any database records or scripts you have created. It will not remember the scripts you created, but they are still where you have saved them.
It will reset and custom workspaces and any custom colors you have applied to your cues, but that's about it.
Let us know how it goes.