ignored files are appearing in my commit options. is this right?

os: kubuntu 10.04
PhpStorm 2.0Beta
build: PS-103.8

in my settings
FILE -> SETTINGS -> PROJECT SETTINGS -> VERSION CONTROL -> IGNORED FILES

I have added the directories .idea/ and compile/ to the ignore section.  Im understanding that this will mean that the version control system (git) should not include these files.

But when i right click on the main project folder and choose GIT -> COMMIT DIRECTORY I get this:

the /.idea/ and the /compile/ directory are both there with check marks waiting to be committed.  Is this correct?  and if so what is the point of adding stuff to the SETTINGS -> VERSION CONTROL -> IGNORE area.

Thanks