I don't know what you did that prevented the shortcut from being created on your desktop, but there are also shortcuts created in the Start Menu. Without these shortcuts, the games will use the default dosbox.conf, not use the custom configuration files created for them, so yes, the games will start in a 640x400 window and will not use the right output to prevent the color corruption that occurs when you set DOSBox to run full screen. They will also be using cycles=auto, which is not good for these games.
Even though the installer is set to run with elevated privileges, UAC may be getting in the way. Try running the installer as administrator (right click on the installer and choose "Run as Administrator".
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