One way in Wavelab 8 and 8.5 is to layout the windows as you want them, with all montages and audio files closed. Then select menu Global > General Window Layout > Save current Layout as Default. Close Wavelab, then hold down the Ctrl key while re-opening Wavelab. You’ll get a dialog. Select “Restore default window layout” and checkbox “Keep answer”. Then it will always open with that empty window layout.
Sounds like something’s stuck. You could try the “Without Files” option in the Ctrl key open dialog, then when that’s open save again as Default Layout, and re-open Ctrl key Default Layout.
There’s probably a pref file that could be deleted in the audio file workspace prefs, but I’d try that first.
Or you can go to the workspace layouts menu and define default or custom named layouts while in the audio file workspace, and in the montage workspace.