Sonarqube 6.2 finds only code duplication, no bugs, vulnerabilities or code smells

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I'm running Sonarqube 6.2 on Ubuntu 16.04.01. When I was running Sonarqube 5.4 everything was working fine. After upgrading to 6.2, I scan my project directories, the analysis completes successfully, but the main dashboard page for each project says 0 Bugs, 0 Vulnerabilities, 0 Debt, 0 Code Smells, but it does find code duplication.

I don't see anything in the logs or config files that would allow the analysis to finish successfully but result in no issues found. I know for a fact there are a ton of issues with the code.

screenshot of dashboard with "0" results

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