There are some instances where the Waves Preferences window appears after Pro Tools has launched and a session has been open. This seems to happen only with Waves 7.1 and recently ProTools 8 versions. To fix this, follow these steps:
1. Quit Pro Tools and all other applications
2. Navigate to Macintosh HD > Users > (your account) > Library > Preferences.
There, locate the Waves Preferences folder and drag it to the Trash.
3. Empty the trash and launch Pro Tools again. Do not open or create a session.
4. When you see the Waves Preferences window appear, make sure that “do not show this prompt again,” is check. Make any other desired changes to Waves preferences and click OK.
5. Do not open or create a Pro Tools session yet. First, QUIT Pro Tools and launch it again – the Waves Preferences window should not appear.
6. Open or create a session and check to see if it works properly.
NOTE – You may also need to avoid using the “Quick Start” window in ProTools which sometimes hides other windows.