Are you reading from a DVD or from files on the HD?
This is from the Shrink help file.
Compress video with high quality adaptive error compensation
When video is compressed, small errors or artifacts are introduced. This is an unavoidable consequence of video compression, and DVD Shrink cannot prevent this from happening. However, it can keep these artifacts to a minimum.
This option will adaptively compensate for any artifacts introduced by the video compression, so as to prevent them from propagating into the next pictures which are compressed. This requires DVD Shrink to dynamically decode and compare both the original and the compressed video, so that it can detect if artifacts have been introduced and compensate for them accordingly.
AEC (adaptive error compensation) requires a lot of CPU power, and depending on the speed of your computer, it may take an hour or more to complete your backup. However, it will often provide a far superior video quality. AEC will also benefit from deep analysis.
If you do this then it will take a long time. I suspect that most users of Shrink don't do this.