I installed Firefox 3.18 and created a new launcher and removed Firefox 4. When I try to minimize all the windows will hide and I can't find them.
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While this may not correct the issue with Firefox, it may help you better deal with it. Tell me, when Firefox is minimized as you have described, what does Alt+Tab buy you? Are you able to select Firefox and begin working with it again?
Please let me know if I have missed the gist of your question, as I am having a little difficulty understanding exactly what you are asking.