When using AutoPIPE with multiple monitors, there are several scenarios in which a window positions will get messed up. One example is the interactive results box will sometimes become very tall, with the results still shown at the top and then blank space which extends downward off the screen. Another example is when using AutoPIPE on the non-primary monitor, the interactive results box will not show up on any screen and it can only be found by unplugging all monitors to reset the position. Another is when using AutoPIPE on a non-primary monitor the analysis progress/warnings boxes will pop up on the primary monitor and can sometimes go unnoticed. One may spend a few minutes wondering why the analysis hasn't finished only to find a warning pop-up on the other screen. All sub-windows should stay with the main AutoPIPE window by default unless moved.