Why is Premiere CS6 remembering past cuts?

Is this a bug?
So throughout my video, I've been cutting, rethinking cuts. Yet, I'm having problems with CS6 remembering old cuts and I can't understand why because they aren't in the timeline.
Example: I cut apart a video. I decided I might want to make different cuts to the video. Redrag video in time line. cut off end. Render clip. In the middle of the clip, there is a big black 3 frame nothing that is not in the original video.
Example: Cut off a few frames of the beginning of a video. Drag another video starting the same time in video 2. Video one shows through for 2 frames despite video 2 being on top (I checked down to the frame. Even worse, the original video is being displayed for those 2 frames instead of the video I cut in Track 1.
It's almost like premiere is trying to remember something for some stupid reason. These ghost cuts are killing me. It's happened all throughout my video, usually 2 frames at the begninng of a clip but not limited to, like in example 1.
Anyone else see this problem?

This is a bug. This for some reason has to do with Motion>Scale.
Once I put the scale down to 33.3333 instead of 34 (making the new size to be exactly 640x480). That is just this particular video though and I have to check whats going on with some of the others as they have no scaling in the motion tab.

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