Lord Grievous said:
I'll try remuxing the audio again, see if that helps. The 14GB mkv you mention, is that also colour-corrected?
You need to re-encode the audio not remux it. Remuxing it won't change anything. :-)
The 14 GB mkv is identical to the AVCHD. It just looks better - not greatly, but it looks better.
@Darth Editous, thank you for the comment, if it was meant for me, but the files I was talking about were already mkv files.