I am running media player 1.2 and noticed recently that if i have .mkv file with aac 5.1 track it is down sampled to PCM stereo. XBMC on the other hand can transcode 5.1 aac to 5.1 AC3. So now i am forced to watch some of the videos via XMBC. Are there any plans of on the fly aac-ac3 conversion for file core media player?
Up. Guys this is really annoying missing feature. Recently i am forced to watch all new movies (mp4 with aac track) in XBMC in order to get proper sound on my 5.1 home sound system. It does not look like something complicated, since it works via XBMC on the same hardware.
This sounds like a bug to me. I would recommend you open a support-ticket http://support.firecore.com/requests/new 
I understand this is an old thread. But this feature is still missing. All 5.1 aac audio is downmixed to PCM 2.0. I can watch through my smart TV connected NAS just fine as 5.1. But this is not as friendly as ATV flash. Also my TV doesnt play .mkv files. So, this is very annoying. Any fix or update on this…?
Haven’t heard anything from filecore guys. Still have to watch half of movies in XBMC because of this 
I use iDealshare VideoGo to convert AAC to AC3 or convert AC3 to AAC with 5.1 channel
Step by step guide at How to Convert AC3 to AAC, WAV, AIFF, FLAC, M4A, WMA, MP3 on Mac/PC?
To make the output AC3 in 5.1 channel,
You may follow the setting below:
Click “Setting…” button, the “Advanced Settings” Window will pop up right beside the main window;
.
In the ‘Advanced Settings’ Window, switch to ‘Advanced’ tab and then go to the ‘Audio Codec’ section;
Click Stereo on the right side of Channels to select 5.1 from the drop-down list.
You may try use Avdshare Audio Converter to convert AC3 to AAC on Mac and Windows