oh ok I understand that perfectly thanks.It only really matters if you're going to use effects, in which case you want to make sure the editor is using the NTSC 0.9 pixel ratio internally, instead of Square Pixels. But resizing the video out to 848x480 means you can use Square Pixels and not worry about the effects looking wrong. It's just a matter of making sure everything matches.
What format is the audio? AC3, AAC, Vorbis, DTS...something else? It's possible (though I don't know under what circumstances) that FFmpegSource simply doesn't support the audio format that was used. To find out, open the MKV in MKVMerge GUI (http://www.bunkus.org/videotools/mkvtoo ... ml#windows). It'll show the tracks and their identifiers, and show what the audio format is.
Thanks for the program by the way, looks very useful. When I open the file in MKVmerge GUI it says that there are video track, 2 audio tracks (I.E. English and Japanese), and and subtitle track. Both english audio track listed says A_AAC (ID_2, type:audio) and the japanese is also A_AAC (ID_3, type:audio)