Given the following analysis set configuration:

Why does this model analyze 5 different times when there is only 3 analysis sets?

Answer: 

Expand /scroll the analysis set dialog to the right in order to see all of the settings. The analysis is performed 5 times as the first two analysis have the "Remove Lift-off Supports" setting enabled, which results in two additional static analysis.

Reading AutoPIPE's help on this setting: "and re-run the analysis..."

Please refer to the help section for complete details on this setting.