Video Editing Software

I need a video editing program that allows me to cut parts out of a video file, saves the final result back into the original audio, video, and container formats, and works well with .mkv and H.264. I've been using Avidemux because it works great with .avi but it really hates .mkv and H.264. What program(s) do this?

 

Apparently a script can be created with Avisynth for .MP4 editing in VirtualDub. I have no idea how to create Avisynth scripts, or how to implement them in to VDub, but it can be done. Personally, when I need to edit MP4 (or MKV) files, I convert them to XViD/DiVX .AVI files first. I haven't found an editor that works well with MP4 and/or MKV files. Besides, I rarely run into MKVs so they're more-or-less a non issue. My home DVD player has DiVX playback ability, so converting MP4 files to DiVX files is definitely preferred (in my house, anyway ). Some good freeware converters are:
Dr. DiVX (converts almost any video file to DiVX; I use this often)
SUPER (converts audio/video to/from any format; I haven't used this in a while)
MediaCoder (convert to/from many formats)
AlltoAVI (OGM-MKV-MP4-h264 to AVI)

 

I run into .mkv a lot because I handle all the acquisitions of unlicensed anime for my college's anime club and a lot of the newest stuff is being released in HD as .mkv w/H.264. What I need a video editor for is so that I can cut out the rest of the show so I'm left with the intro/outro for when the club is out trying to attract new members at various fairs on campus. I would just convert the files to .avi buuuuuuuut the it takes too much extra time to do.

Why don't a lot of video editors support .mkv and H.264? Even Sony Vegas doesn't do them natively (last I checked any way.) It's not like either format is hot off the press or anything like that.