Java class not found:
The problem came with the cumulative update 9. The "java runtime Engine" is automatically started with Studio to improve the functionality of multiterm. This standard setting causes now this problem with inx files, but can be switched off:
in Tools > Options > Java Runtime Engine Startup (see screenshot)
uncheck the option "Start Java Runtime Engine when starting up SDL Trados Studio" and restart Studio.
Now, you can prepare your project.
...Don't forget to check the box again if you plan to work with terminology in the editor...
More information in http://kb.sdl.com. Search "cumulative update studio"