Tried new FlashFXP and had this same very problem in Win XP and it only happens when you stress computer like put something taking most of processing power like video encoding example and then try to minimize FlashFXP then you never get tray at all but first time you minimize it to tray it works everytime even when lot of processor power is used. So fault seems to be in FlashFXP code. It probably doesn't do everything like it should second time it's minimized.
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