Well it would appear I have solved it. It was neither GPU Audio or NTFS. It was the CPU. Turns out a 4ghz overclock was functional enough to appear stable, but really it wasn't. This also explains the occasional freeze I got whenever installing OS X.

I turned it down to 3.6ghz and I can watch YouTube for hours and edit RAW images happily without a fuss

Just a warning for those who overclock I suppose