We have the same issue but it isn't the TDM or RTAS filters that it is trying to start, it's the Audio Unit files and it seems that FCP can't handle something inside the Waves plugs (I kept getting the message from FCP that the plugs were out of date!).
Our solution was to make a folder just outside the Components folder in Library>Audio>Plug-ins, that I called Problem plugs and pull the Waves AU Waveshells into it. We only use the RTAS/Audosuite plugs with ProTools
I purchased Wave Arts plugs to use IN FCP as the Waves plugs didn't work in version 4 or 5 (Waves that is, not FCP 4 or 5). If I need the Waves plugs in an app like Amadeus Pro or Soundtrack, I pull the Waveshells back into Components - seems a drag but it's too difficult getting Waves to understand and do something.