Hi Simon,
I found this thread as I’ve also been looking for solutions to this problem for a while now.
I have a gopro hero 3 black camera – always recording in protune mode, using a win7 64 editing station that isn’t anywhere near as powerful as yours, but can quite happily edit 1080p DSLR files.
It’s probably not your system. I have the same problem in premiere 6, but not in premiere 5.5.
I had no problems with the gopro files in 5.5, and still don’t. But when I upgraded to CS6, I noticed the problem straight away. There is some compatibility problem on either gopro’s or adobe’s end.
For the time being, I convert my gopro files with the cs5.5 encoder to another h.264 file – which then work flawlessly in cs6.