It was a long WTF moment and I could not find any information on the issue, so I decided I put it here.
Setup: Windows 7 x86_64, sonarqube-4.3, sonar-runner-2.4, jre 1.7.0_55-b14
I followed quick start guide to configure Sonar.
I copied sonar-project.properties from a sample to my solution, put it in the directory with .sln, and made necessary adjustments:
sonar.projectKey=org.whatever.project
sonar.projectName=Project
sonar.projectVersion=2.0
sonar.sourceEncoding=UTF-8
sonar.sources=.
sonar.visualstudio.enable=true
Problem: Analysis ran without any exceptions but only C# files were analyzed.