Problem Encoding H.264 MKV Video

[hddvd2]

I have some videos with H.264 in an MKV container. I am trying to encode these videos to DVD. I am using a Script since no encoder i know of takes H.264 and MKV. Here is my script:
#ASYNTHER DirectShowSource
DirectShowSource("C:\Documents and Settings\Ravin\Desktop\1.avi",23.976,audio=false,v ideo=true)
Lanczos4Resize(656,448,0,0,640,480)
AddBorders(32,16,32,16)
ConvertToYUY2()

when i put that in CCE it looks like it encoded all of the video. It has all of the frames right and the time right when i am in CCE. But the output file ends at about 21 min 40 sec of the video which is 22 min 49 sec. After CCE finishes the encoding i load the file in Virtualdub and the time reads 22 min 49 sec and the frames are also correct, but the video finishes at the point of 21 min 40 sec . Can someone please help me? any help would be great.

[hddvd2]

well i tried cutting the mkv file, and the same crap keeps on happening. i try to cut the credits out with mkvmerge GUI but it always goes into like 10 sec of the credits. I also tried the trim filter in avisynth and the same exact thing happend. Someone please help me. It is strange because the place where i want to cut is right at a chapter point. (I also removed the chapters, but i still have the same problem)