Here's the crazy part. I'm muxing the AC3 5.1 with the encoded x264 video stream using MKVMerge and when I play back the final MKV...I hear the Director's Commentary. And to further complicate it, when I playback the unmuxed 5.1 AC3 file by itself, it's as it should be.
Sound like what is happening is haali splitter is defaulting to the Director's Commentary instead of the primary ac3 stream. Are both muxed into into the mkv? If not is the commentary in same directory as the mkv? To solve your problem, when muxing the streams set the ac3 file as default under the general options in mkv (with the stream selected in the main window) and remux. If your commentary track is in the same directory as your mkv and it is haali that is picking it up and playing it as the default track then you can do one of two things:
1. Go into the options for haali and disable the option to associate audio files with video files (sorry can't remember of the top of my head what it called, not near a windows PC!).
2. Rename the audio file that is causing the problem to something else different from the mkv.
I'll answer your Qs in order:
1. Yes it is normal to end up with a larger flac file than DD+ ....the efficiency of flac is about the same as TrueHD/dts MA/dts HD and obviously you stand to gain significant saving with LPCM since this is not compressed at all.
2. Dts @1.5 Mbps from DD+ will be very simular to any studio created tracks, its doubtfull you will be able to hear a diff and since dialogue normalisation will be removed in the process it will actually sound more agressive than the DD+ track you started with. Thier will be some difference however between the dts and DD+ track since DD+ is more efficient than legacy dts. (ac3@640kbps is also much better than most DVD tracks due to DN removal and higher bitrate).
3. Dts HD is supported in mkv now, you can mux a dts HD/MA track into mkv with mkvmerge but the problem is arcsoft filters and any other COMMERCIAL players will not decode the tracks when they are not in Blu ray or HD DVD file types/structures (player dependent) and will still downres sound anyway withour PAP. You may be able to get this working in Directshow with the filters (I know its possible, I've done it but its a ball ache and not worth the effort when flac is so easy). At the min flac really is the best and easiest way to get full resolution, full bitdepth sound. In essence you do get dts MA/HD with flac as the decoded info is the SAME bit perfect LPCM stream.
4. You will need to get rid of any resize options but that is it so don't tick the 'clever anamorphic resize' option and thats it. Happy encoding!