I'm not sure what you are describing. I'd ask for a picture, but...invisible.
Two ideas:
- can you show a picture of the home window when an invisible window is open? The icons might give a hint.
- did you have a 2nd monitor, and perhaps remove it? Maybe a laptop that was docked? It could be JMP is remembering where the windows were the last time, on the other monitor. There is a way to move a window with the keyboard (no mouse) that can get off-screen windows back again. I'm not sure where JMP keeps that information. Renaming the file to something JMP hasn't seen before could also fix it.
edit: what OS, what version of JMP?
Craige