I suspect that the encrypted partition isn't indentifiable as a removable USB device (which is what Opus looks for); possibly TrueCrypt is presenting it as if it were a fixed disk, and so Opus doesn't recognise it.
The Opus licence that is exported is already encrypted, and also locked to the device it's exported to, so no one can steal your licence if they steal your USB (although they can, of course, plug it in and run the program off of it).