Because it was too difficult to type this out I made a short video to show the problem. http://www.youtube.com/watch?v=Cr7C2vdTaHQ
Things to know:
1. It doesn't matter how this is built, this issue occurs regardless.
2. The commands to the command blocks are in the description.
3. The issue is that the comparator that is connected to the 3rd command block (the one with 3rd command listed below) does not turn off when it is supposed to. The only way to get it to turn off is to break the command block, or to right click it.