Hello,
I have the same issue. I can play m4a files perfectly fine (with an m4a extension) but they are not displayed in the Amarok file browser.
I am using:
Amarok 2.5.0
KDE 4.8.3
Phonon 4.7.0really4.6.0-0ubuntu1
Phonon GStreamer 4.6.0.
I have several plugins installed included the Gstreamer bad and ugly.

Apparently the main difference is that I am using GStreamer back-end (which comes by default with a clean install of Kubuntu 12.04). I could use the vlc backend but for some reasons the playback with vlc has been crackling lately so I'd rather keep Gstreamer for now.
I can file a new bug report if I did not miss anything and this is actually a bug.

Thanks

vdeparday - it's a bug (imho), should be filed in phonon-backend-gstreamer not Amarok

this bug report's comments includes confirmation https://bugs.kde.org/show_bug.cgi?id=268896#c10 which would useful in the report