When the program we are using for an installer performs a "Repair", it basically does an uninstall and then re-install. The point where your anti-virus appears to have popped in is where the installer is finishing up the uninstall and then beginning the re-install. If for some reason a file can't be deleted by the uninstall it may schedule the uninstaller to run after a reboot to complete the process which is my best guess for why this is flagged as a virus at that point. Typically this only occurs if the "ieflash.dll" which is the browser plugin for FlashFXP can't be deleted because a browser is open. I'm not sure if this plugin is also used by firefox or not but I do see that browser open in your image.
The version on our website has been scanned by multiple scanners and should be clean. I am curious if when you run the setup.exe file with UAC off, have you tried running it "as administrator" and if so did it have the same report or did it have the same problems once it was installed?
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