The expand folder feature was designed so that when you expand your queue only the folders for the connected site are expanded, otherwise FlashFXP would disconnect you from the current site so it could expand folders on other sites. Perhaps this could be an additional option, but until then it will only expand folders for the current site.
Without going into a whole lot of details, there are some legacy issues that prevent us from reliably establishing a connection at this specific moment, this prevents the expand folder feature from connecting to the site for you. I will do my best to find a solution to this in future releases.
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