I am using intellij 14 with scala 2.11.6 installed using home brew and symlink using
ln -s /usr/local/Cellar/scala/2.11.6/libexec/src /usr/local/Cellar/scala/2.1
I had the same issue than you experimented and the solution, actually very easy, was actually erasing the .idea folder from the project, the problem is that the configuration inside of this folder (containing the set ups for example for the test, VCS, the runs, etc) gets corrupted with double entries (probably cos you update your Scala version), once you do this and reopen the project in Intellij the IDEA will generate a fresh new configuration for you.