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1) When I click Show Desktop....
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The reason FlashFXP behaves differently is because it was written in Borland Delphi, Borland Delphi applications are slightly different compared to applications compiled under say MSVC.
The difference is that Delphi applications have a seperate window for the taskbar button which is seperate from the main form.
And because of this minimize/restore/maximize work slightly different.
In order to provide the necessary auto minimize to tray we have to hook a window message that is sent to the fake hidden window on minimize. When you select Minimize All Windows it causes the same message to be triggered and FlashFXP goes to the tray.
There is no way to tell the difference between a minimize by FlashFXP or Minimize All Windows.