On HP passes the first generation wizard only controls the boom at the start of the pass, not the rear. When a boom goes down at the back of a vehicle, that is the start of the pass before the gantry goes towards the front. It controls the down time in seconds. It is not looking at the proxes to determine how far to go down, there are there to serve as limit switches.
Lets say the passes you are describing in the above scenario is pass three and four. In pass three when the boom goes to the bottom prox the boom down time is probably set to 8.0 seconds, which will force the boom to travel down eight seconds (or until it hits the bottom limit switch). The repetitive up and down motion is caused by setting the option on the menu called "bug pass". On pass four, the boom is probably set to around 5 seconds, with no bug pass selected. You can enter programming and change this setting if you know how to program one.