I've run into this issue now a few times, and it appears to be limited to the script step and scripts manager "floating palettes" and doesn't seem to affect other palettes such as the Inspector or Field Chooser.
So, what happens is, if I am trying to define a button, for exmaple, the palette for a single-step button operation (or for a script) does not appear on the monitor, but is still active and waiting for some interaction. At this point, FileMaker won't accept any input nor can one use ESC or any other action to get out of that mode.
At first, I thought it was only because in a previous session, I was using dual monitors and had some of these dialog boxes on the 2nd monitor. However, the other day, I was using dual monitors but had the main FileMaker screen on the 2nd monitor, and wham, tried to define a button and was stuck! See attached screen shot.
Clearly, if the monitor configuration changes from one session of FM to another, a routine needs to occur so that all pop-up palettes or dialog boxes are displayed on the active monitor(s). Clearly this DOES happen with Inspector and Field Chooser palettes, but not with Button / Script palettes.
It's driving me crazy to have to force kill the FM Pro process (I'm using the latest FM Pro 14.04 version).