Waves knows about this issue on 64-Bit systems. It's usually related to the fact that when you install the Waves plugins, it may install both 32 and 64-bit plugins. Here's what happens:
WaveShell installs in your 64-Bit directory, hopefully.
The actual plug-in files will attempt to be installed in both the Program Files/VST and the Program Files (x86)/VST directories (or similar). You have to "hide" the
32-bit plug-ins from Sonar. If it sees them, it has a difficult time trying to do (something), and there isn't yet an actual fix for this. After hiding the 32-bit Waves plug-ins, you'll need to re-scan your plug-ins. You may even have to Reset all your Plug-Ins.
It's hit or miss after that, but if you call Waves Support, they can access your system and fix this for you. Hope this helps!!