If you do not want to upgrade an existing Windows 3.x installation during Unattended Setup, you should hava a Win31Upgrade=no in your unattended answer file.
You must also hide the old Windows installation from Windows NT Setup. If you don't hide it, setup will only honor your Win31Upgrade=no if it has insufficent room on the Windows drive or if it suspects that Windows 95 is installed. If it finds Shell32.dll, User32.dll, Kernel32.dll, and Gdi32.dll in the system directory, it will think W95 is installed.
If setup finds Win.com, Win.ini, or System.ini the Windows directory, and autoexec.bat in the root, it will think Windows 3.x is installed.
Since setup only searches for Windows in the PATH as defined in C:\autoexec.bat, the best way to hide the Windows 3.x installation is to edit autoexec.bat and remove all reference to Windows from the path.