After a while I got Waves working in my PC with Windows 7 in ProTools 9HD, it was kind of tricky. Note: I'm from Argentina, and my Windows is in Spanish, so I'm translating textually all folders and commands, so they may be named different in your PC, but I think the names will be close enough to the english version.
1º First backup all your waves presets (C:\Program Files\Waves\Plug-Ins\Plug-In Settings);
2º Uninstall all Waves bundles;
3º Run "regedit" and ERASE these entry from the registry:
HKEY_LOCAL_MACHINE\SOFTWARE\Waves
4º Erase all these folders:
C:\Users\{username}\AppData\Roaming\Waves
C:\Users\{username}\AppData\Roaming\Waves Audio
C:\Users\{username}\AppData\Roaming\Waves Preferences
5º Erase ALL files with *.dpm, *.xml and *.rsr that are named "waveshell" inside:
C:\Program Files\Common Files\Digidesign\DAE\Plug-Ins
6º Theres a known issue between Internet Explorer and ProTools. Theres a Registry Tweak that I downloaded a time ago from another Forum, and you can download it from
http://depositfiles.com/files/k3lppq98g. I've been using it and haven't had any trouble, but I don't make myself responsible for any problem it may cause to your computer!! (It disables DEP from Internet Explorer 8 & 9);
7º Reset your PC;
8º Reinstall Waves;
9º Go to Language and Regional Options in Windows and make sure that in Regional Options -> Personalize you have these 3 things:
Decimal Symbol: , (coma)
Thousands separator: . (dot)
List separator: , (coma)
10º Reset your PC;
After all that, I ran ProTools and Waves worked perfectly!!
Hope this works fine for you too!!