There is no option to minimize on connect, there is however one to restore FlashFXP on connect. I'm not quite sure why you'd get the opposite effect, my best guess is that the problem is occurring from something else.
We're preparing to release FlashFXP v3.6, we're currently at RC2 and we'll be releasing RC3 next week. v3.6 makes many many improvements for windows vista users. You might consider upgrading and perhaps it will solve the problem.
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