I don’t think Whonix 11 → 13 upgrade has been well tested. You should probably install the latest distribution.
The error is unrelated to FPM2. Error is caused by whonixcheck running in the background. See if running FPM in a terminal produces any meaningful output.
FYI anyone who cares, protobuf is Google’s Protocol Buffer parser. It’s most likely installed using Python’s PIP tool.
@ramongalaxy
Profile: /usr/bin/whonixcheck Operation: Open DENIED Name: /usr/local/lib/python2.7/dist/package/protobut-2.6.1-nspkg.pth