Well, I have figured out the problem here if anyone is interested.
I have ditched Premiere Pro CS4 for now and have picked up Sony Vegas 9 Pro (trial). Exporting in a Quicktime container with MPEG-4 codec using 60FPS and 100% quality get's me an identical output from the raw .MTS files.
Just trying different audio outputs and different quality settings to try and find the sweet spot between quality and size.
Drawback is that it takes quite a while to render/export.