Best guess is that you have something else running that takes priority and pushes FS9 to the taskbar. This may be something kosher (Windows related) or you may have a virus/Trojan running in the background; next time you got to run FS9 start the Task Manager before you do, then you'll be able to see what else is running if/when it minimises. I'd also do a full system scan with decent AV and spybot programs if I were you.
Hope it proves to be something relatively straightforward.
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