Hi @dgh,
I’ve moved your post to a new thread so it will be easier to investigate. (Feel free to edit the title. 
) Would you mind posting a debug (-Dsonar.verbose=true on the analysis command line) log?
The analysis / scanner log is what’s output from the analysis command. Hopefully, the log you provide - redacted as necessary - will include that command as well.
This guide will help you find them.
Thx,
Ann