HI,
I too have experienced this problem, i don't think its a hardware or osx issue. My set up is a bit different to everyone who has posted on this issue so far.
So i thought it might be helpful to throw in my two cents worth ...
I have a CustoMAC other wise know as a Hackingtosh to the uniformed, based on a Gigabyte H77N motherboard which is one of the very few that offers
(almost) perfect HDMI video and audio osx integration. i built this system to replace an old Apple MiniMAC running 10.7.5 because i was having all sorts
of issues with muti-channel sound in XBMC, if your interested in it see
here
Anyway after replacing the old with the new i am now running OSX 10.8.4 the very latest version of OSX
its got an i3-3225 CPU using intel HD4000 GPU
the only connection to my amp is via HDMI to a Denon AV Amp
I have set OSX default sound output to HDMI in System Preferences/Sound/Output
In XBMC i have set all audio outputs to default sound device
Speakers should be set to 2.0, this was something i found out when researching my previous thread, its to do with the bit stream which is basically a dual channel PCM stream, the multi channel info is inside this dual channel stream so it needs to be passed untouched for your amp to decode it correctly. read my other
thread for a bit more info of how i came to use 2.0 and not 5.1 even though my setup is a 5.1 system
all hdmi passthroughs DD/DTS/LPCM should be enabled
with these settings i get perfect video and audio playback, no stuttering, perfect sound after a pause, forwards, backwards, chapter ..etc all perfect.
If i set speakers to 5.1 same thing happens to me as everyone else here, playback starts to stutter after about 45 mins, it did it with all types of video - mkv/avi and all types of codec DD/DTS/AAC
For sure the Apple audio API is a mine field as they do things differently to everyone else but thats apples way.
The main issue is the speaker setting, anything other than 2.0 seems to be an issue,
Its also possible that by setting XBMC's' audio outputs to default, and having the osx system default setting set to HDMI may solve the issues when resuming playback from paused.
It works for me, and its been a struggle to get here after the problems of my last MAC but right now everything works perfect with this setup
Good luck to you all and a big thanks to the dev's without whom we wouldn't be here
I'm currently running the stable frodo 12.2 release, i tried the nightly's and they all did the same thing at least up to last week they did.
Cheers
Jay