You can clone with
"Sometimes it seems like FontForge is not responding when you are in the Glyph Window. What might be occurring is that there is an open dialog box hidden behind the Glyph Window. You will then have to move the Glyph Window to see the dialog, dismiss it, and return to the Glyph Window."
This annoying quirky behaviour should be fixed.
They should float above if and only if they are modal. Modal dialogues invisibly eating input, as described, are a problem, but I hate nonmodal "palette"-type things that I can't shuffle behind other windows.
Closely related: nothing should be modal unless it must be.
Not so closely related: I wish I could close the "Warnings" window and have it stay closed.