Most likely the shortcut you're using to launch FlashFXP was a custom shortcut not created by the installer or during installation you unchecked the options for FlashFXP to create/update the Start menu or Desktop shortcuts.
The 4.x version of FlashFXP installs into a new folder by default.
The default program folder is C:\Program Files\FlashFXP 4\ or C:\Program Files (x86)\FlashFXP 4\ on Windows 64 bit.
You'll need to create a new shortcut or update your existing shortcut to point to the new installation of FlashFXP.
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