[mjr4077au]

OK Here's an elaboration of whats going on and what messages I get.

First I add all tracks and subs into each movie with mkvmerge. Then I mux them with AVI-Mux GUI. The file I get plays fine.

Then I try to re-mux the file with mkvmerge as I think AVI-Mux GUI is dodgy (And evidently, it is). This is what I get

Warning: 'C:\Documents and Settings\Mitchell\Desktop\lets hope this works 2.mkv' track 3: The current packet's timecode is smaller than that of the previous packet. This usually means that the source file is a Matroska file that has not been created 100% correctly. The timecodes of all packets will be adjusted by 504ms in order not to lose any data. This may throw A/V sync off, but that can be corrected with mkvmerge's "--sync" option. If you already use "--sync" and you still get this warning then do NOT worry -- this is normal. If this error happens more than once and you get this message more than once for a particular track then either is the source file badly mastered, or mkvmerge contains a bug. In this case you should contact the author Moritz Bunkus <moritz@bunkus.org>.
Warning: 'C:\Documents and Settings\Mitchell\Desktop\lets hope this works 2.mkv' track 4: The current packet's timecode is smaller than that of the previous packet. This usually means that the source file is a Matroska file that has not been created 100% correctly. The timecodes of all packets will be adjusted by 504ms in order not to lose any data. This may throw A/V sync off, but that can be corrected with mkvmerge's "--sync" option. If you already use "--sync" and you still get this warning then do NOT worry -- this is normal. If this error happens more than once and you get this message more than once for a particular track then either is the source file badly mastered, or mkvmerge contains a bug. In this case you should contact the author Moritz Bunkus <moritz@bunkus.org>.
Warning: 'C:\Documents and Settings\Mitchell\Desktop\lets hope this works 2.mkv' track 5: The current packet's timecode is smaller than that of the previous packet. This usually means that the source file is a Matroska file that has not been created 100% correctly. The timecodes of all packets will be adjusted by 504ms in order not to lose any data. This may throw A/V sync off, but that can be corrected with mkvmerge's "--sync" option. If you already use "--sync" and you still get this warning then do NOT worry -- this is normal. If this error happens more than once and you get this message more than once for a particular track then either is the source file badly mastered, or mkvmerge contains a bug. In this case you should contact the author Moritz Bunkus <moritz@bunkus.org>.
Warning: 'C:\Documents and Settings\Mitchell\Desktop\lets hope this works 2.mkv' track 6: The current packet's timecode is smaller than that of the previous packet. This usually means that the source file is a Matroska file that has not been created 100% correctly. The timecodes of all packets will be adjusted by 504ms in order not to lose any data. This may throw A/V sync off, but that can be corrected with mkvmerge's "--sync" option. If you already use "--sync" and you still get this warning then do NOT worry -- this is normal. If this error happens more than once and you get this message more than once for a particular track then either is the source file badly mastered, or mkvmerge contains a bug. In this case you should contact the author Moritz Bunkus <moritz@bunkus.org>.
Warning: 'C:\Documents and Settings\Mitchell\Desktop\lets hope this works 2.mkv' track 2: The current packet's timecode is smaller than that of the previous packet. This usually means that the source file is a Matroska file that has not been created 100% correctly. The timecodes of all packets will be adjusted by 421ms in order not to lose any data. This may throw A/V sync off, but that can be corrected with mkvmerge's "--sync" option. If you already use "--sync" and you still get this warning then do NOT worry -- this is normal. If this error happens more than once and you get this message more than once for a particular track then either is the source file badly mastered, or mkvmerge contains a bug. In this case you should contact the author Moritz Bunkus <moritz@bunkus.org>.

If I append both files with mkvmerge, I get this:

Warning: The track number 2 from the file 'C:\Documents and Settings\Mitchell\Desktop\tlotr_ttt__2.mkv' can probably not be appended correctly to the track number 2 from the file 'C:\Documents and Settings\Mitchell\Desktop\tlotr_ttt__1.mkv': Please make sure that the resulting file plays correctly the whole time. The author of this program will probably not give support for playback issues with the resulting file.

The Return of the King is still ripping so I haven't tried that but by using the first method with AVI-Mux GUI and then remuxing it with mkvmerge, I had a perfect file. What should I do?