I don't know what is causing this issue, as far as the box being hidden, but once that box popped up real quick, I couldn't put other things on top of the window by clicking on anything, including task manager. I had to set the task manager to always on top to kill Firefox. Maybe someone can give me a clue as to why this is.
Anyway, I got my bookmarks imported by upping the time in Miscellaneous as stated above by Chuck.
Thanks for the help.