I am experiencing the same type of problem.
However I do not thnk it is minimize related. My FlashFXP build 908 has been running for some days (uploading to a very slow site) being opened from the try icon area and minimized again.
Then it just went missing.
The only way to see the window is when FlashFXP brings up a confirmation dialog when the site I am uploading to got disconnected and FlashFXP asks to resume. Minimizing again and the icon is missing.
System: Registered FlashFXP, XP Pro SP1, hide inactive icons enabled.
Bug?
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