Solved! Go to Solution.
Solved by ryan. Go to Solution.
Switching profiles does a few things with workspaces... try about halfway down this thread: http://forums.autodesk.com/t5/AutoCAD-2013-2014-2015/how-to-PERMANENTLY-AND-FOREVER-turn-off-the-Nav...
The items you mention automatically loading are likely coming through using the .bundle auto-loader mechanism.
Also, check your settings for saving workspace settings. If its set to automatic then anything which constitutes a change will prompt a save. That includes previously loaded CUIx files not being present.
I found the information about the .bundle deployments which solved the problem; http://docs.autodesk.com/ACD/2013/ENU/index.html?url=files/GUID-5E50A846-C80B-4FFD-8DD3-C20B22098008...
Much thanks for pointing me to the right place to look.
-Ryan