Found a problem which also occurs with latest RC3 when used on a Vista system which also has the utility FileBox eXtender installed. Latter can be found at
http://www.hyperionics.com/.
Problem is when you open Site Manager and either Connect to a site, OR, just click the Close button, the whole FlashFXP window minimizes to the tray. It does not minimize when I carry out other actions within Flash FXP, or just connect using the standard connect button. Temporary fix is to add FlashFXP.exe to the exceptions list which is available within FileBox eXtender.