Did you port the CYFISNP stack yourself or are you using the project from Cypress?
The project is available in the Github for download - https://github.com/cypresssemiconductorco/WUSB
This project was developed in Creator 2.2 and I have tested in Creator 3.0. The project works in both the build. We havent tested in other Creator versions. So try using the Creator3.0 .
Are you in debug mode when you are seeing 0x00 . Can you try using UART and print out the register values instead of checking it in Debug mode ?
Isn't the answer a bit late?