Compressor creates artifacts at the beginning of clip. Then they go away...

So I make calculus videos and I having the file sizes small is important to me but when I compress my videos they have large artifacts in the beginning which then go away after about a minute. Any idea how to prevent this? If I raise the bit rate more they will go away but I would like to keep it low and i don't know why the artifacts go away after a while and it looks fine. Here is an example clip that shows what I'm talking about. Doing a multi-pass also helps a little but not completely.
http://www.guillermoteaching.com/filechute/intsublectureshort-medium%20200.mov
Any ideas?

but i want the motion in the beginning
Is there a way to do an adaptive compression that compresses the beginning at a slightly higher rate or is this just something I have to live with...

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