Harmy said:

Actually, I'm planning two MKV versions, the main one with 15000Kbps BD compatible stream and lossless audio and then another, cropped to 1280x542 at a much lower bitrate with the same audio options as the AVCHD for those, who want a more compact MKV version of around 5GB (it's preferable to people making their own smaller encodes with crappy settings from an already re-compressed source) - I could technically already release the smaller MKV now but I don't want people thinking it's the main MKV release.

Harmy, this is actually great for me! Previously I would have to remux the AVCHD to use get a compact (~6-7gb) MKV for streaming purposes to avoid compressing the video a second time on the larger MKV. I would then archive the larger MKV on blu-ray disc. I know this is asking a lot, but any chance you would do a smaller MKV release as well for SW 2.5? I am continuing to have issues remuxing that file as well. I will try tonight as you suggested demuxing first and then using mkvmerge.