I have quicktime alternative installed not quicktime if that makes a difference.
I wonder if this would cause a conflict. Try specify filters:
Tools -> Options -> Playback -> Video -> DirectShow Playback Settings...
(this is where you checked m4a box). Make sure m4a is selected (highlighted), and click Select Filters button. Wait for the Select Filters window to appear.
On the left side "Source Filters", select "Haali Media Splitter".
On the right hand side ("Other Filters") select FFDShow Audio Decoder.
Click OK.
If that still does not fix it, you may need to open FFDShow's configuration (All Programs -> Combined Community Code Pack -> FFDShow Audio Decoder Configuration). Click "Codecs" on top of the left pane. Make sure "AAC" on the right pane is set to "libfaad2" (and not "disabled").