This issue is still under investigation.
When you start FlashFXP as it populates the local browser it needs to enumerate the files/folders to generate the listing, depending on the anti-virus software it may want to scan each and every file. Not only does FlashFXP duplicate the file listing but it also loads and uses 3rd party shell extensions that you would normally find in windows explorer.
Typically anti-virus software can cause long delays when clicking on a local file.
There are a couple applications you could try to use to better understand whats going on, if we could reproduce the issue we'd be using similar applications to diagnose the problem.
Process Explorer:
http://technet.microsoft.com/en-us/s.../bb896653.aspx
Process Monitor:
http://technet.microsoft.com/en-us/s.../bb896645.aspx
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