To help us investigate, it would be interesting to get logs of both scanner and server side processing, in debug mode.
For Maven or CLI scanners, just add
-X to get verbose logs.
To get compute engine (server side) verbose logs, go to the system info page, and change log verbosity to debug, just before running the scanner. Once the background task has been processed, get the logs and reset to normal verbosity.
You can send the logs to me privately if you are concerned about privacy (julien.henry at sonarsource.com).