I´m currently using a lot of Prompt for user inputs for work and my setup is a macbook with 2 screens.
The window that pop up does not follow a pattern I have recognized.
Usually I have 30 seconds of KBM doing stuff and my mind sometimes (all the time) wander off in wait for the prompt… And when it pops on the screen to my right, I often miss it.
I think my problem was that I had Chrome in full screen mode and the window couldn´t overlap so It found somewhere else to go. It works much better now when not inn full screen mode.
Thanks @JMichaelTX - You got me on the right track