There are an issue http://youtrack.jetbrains.net/issue/SCL-2559.
This is very important issue, and I should write small announcement about it.
Like in Java, our Scala editor wants matching classes package structure and directories structure. This is very important for performance reasons. If this convention is broken in your project, you may see many red code now.
However, sometimes conventions are different in Scala (I'm not sure it's really right). So I added the setting to avoid problems described above. But you should be sure that you really need it, because editor performance can become worse.
Also for fixing problems with wrong packages I added inspection about it.
This changes will be available from build 0.3.354.