And to confirm, the protofile is being registered just prior to the above:
Kinda strange, but I got it to work. For what ever reason, the registering of the protofile by calling the above InputStream wasn't working, but no exception was being thrown. Not until I changed it to the correct class (InfinispanConnectionImpl) did it read it correctly and the marshallers were able to register.
Sorry to waist your time.