You have to understand how MPEG works. I-frames are complete self-compressed self-reliant frames, J-frames only have the "changes from previous" previous frame info and B-frames have info about frames either side. An MPEG stream will have a pattern of I,J and B frames say IJJBJJI or whatever.
B and J frames can't exist without their nearest associated I-frame so if you CUT between I-frames (in MPEG, every 15 frames) you can potentially loose up to seven frames (depending on pattern) back as far as the last I-Frame. So all frames after will be black. Once the stream is disrupted in this way, you get your glitches. The best way around this is to uncompress, ie: export (the file) to the desktop with the NONE compressor, do your cutting, and then recompress with your MPEG (Probably Heuris) compressor. While you are uncompressed each frame is standalone and unique, you can cut where you like. But you need lots of ram and HD space. A 5meg Sorensen QT.mov could be 70megs or more uncompressed!
Some things are easier to do within Premier or whatever rather than just using the Quicktime interface.