We use SonarQube 5.3 to analyze our C# code. The analysis is triggered from the vNext build on TFS 2015 (on premise). We have a quality profile with rules from the C# analyzer plugin (Sxxx) and some FXCop rules (CAxxxx). We've made a .ruleset that reflects the quality profile to be able to run the code analysis from Visual Studio 2015.
However I'm missing some code analysis warnings/errors in SonarQube that are showing up when running the code analysis locally and also show up in the build log. Both in the MSBuild output that is visible when the build is running on the server, as in the [AssemblyName]CodeAnalysisLog.xml.
The weird thing is, we've been solving a lot of issues lately and we have solved several CA1725 issues that were visible in SonarQube. Now we have a number of CA1725 issues (not suppressed) still visible in the logs and the XML, but they don't show up in SonarQube.