It depends on how you start AutoCAD. Most people will start AutoCAD by clicking on the shortcut either in the Start menu or on the desktop. In each of these shortcuts, there is an option to specify the default profile to be used and AutoCAD will generally install with their generic one. If you change the default profile in the options and then use the standard shortcut, then the AutoCAD default profile will be used.
To solve this problem you have actually 2 options.
You can create a new shortcut to the Acad.exe file with no profile set as current, then set the current profile in the options dialog. You will need to do this for the shortcut on the desktop and the one in the start menu.
OR
You can open the shortcut properties of each of the two shortcuts and on the shortcut file where the target file name is located, it will have a command line option for a profile that will be similar to this:
/p "C:\Program Files\Autodesk Architectural Desktop 3\adt.arg"
If it does, you will need to change/verify the path to the *.arg file you created when you exported your new profile and make sure the new profile name is correct in the shortcut.
The above example is the standard for ADT 3.3, and others are similar. Pre 2002 releases of common AutoCAD did not to the best of my knowledge have the profiles in the shortcuts, but desktop packages such as ADT and LDD do use them in the default shortcuts.
Now, if you double click on files to open them rather than open AutoCAD first, then if you set a profile current, it will always remain current.
I hope this solves your problems.