I'm getting the impression that Civil-3D installation includes some undocumented steps. The crux of the matter seems to be that C3D creates a default profile called "<<Unnamed Profile>>", which doesn't work well because of the greater-than and less-than symbols in the profile name.
So, I take it that the default profile should not be used, and the following steps should be performed immediately after installation:
1) Create a new profile, e.g. a profile named "C3D".
2) Customize this profile as desired, leaving the default Unnamed Profile untouched.
3) Open the desktop shortcut, right-click and select "Properties". In the "Target" for the shortcut, change the profile name from the default Unnamed Profile to "C3D".
4) Open the shortcuts in the Start Menu, and perform the same change as in 3).
This seems to make everything work better. It even keeps things from getting messed up when installing SP1 - well, most things, anyway. After installing the SP, the current profile is once again switched back to the Unnamed Profile, but the "C3D" profile still exists, and all the user has to do is set the "C3D" profile current to return to normal.
Sound about right?
Sinc