We had a drafter open a drawing and all the settings in his drawing were not the same as they should be.
We use AutoCAD Mechanical 2013 and Synergis Adept.
The person in my department that is the "CAD Admin" says that AutoCAD should only be opened from the icon. If it is opened any other way that it doesn't load everything programmed to that icon.
I have been opening AutoCAD form this program daily and have yet to see any problems that I didn't cause myself due to not paying attention.
Is there anything that loads specifically through the icon that would cause AutoCAD to load differently?
Check the command line arguments. With verticals such as Mechanical, its not unusual to load a DBX or ARX via a command line switch (\ld "c:\blah\blah\some filename.dbx") which differentiates it from the "Run as AutoCAD" version. There may also be a profile name specified (\p "Profile name") which can also dictate the environment. If you only use one profile, it doesn't cause many problems - AutoCAD will launch with the last used profile. But when you have multiple profiles with different applications, different applications being loaded at start-up (via that \ld switch), and so on, using the desktop shortcut to launch the program first is usually the best course.