what is the version of Scanner for MSBuild you are using?.
what are the commands you are running to do the analysis? are you running all commands from the same folder?
what is the version of MSBuild you are using?
please give us the verbose output of the commands (please run SonarScanner.MSBuild.exe begin <....other params....> /d:sonar.verbose=true as the begin step, and please attach the output of END step)
could you please share the .sonarqube\conf\SonarQubeAnalysisConfig.xml and the .sonarqube\conf\sonar-project.properties . Please note that the .sonarqube folder is in the directory you run the analysis from.