To confirm/disqualify if the startup delay is related to the file listing, open flashfxp, make sure both sides are set to remote view, close flashfxp so that it saves the layout, then reopen flashfxp so that upon startup it has both sides as remote views. Opening this way should not require any directly listing procedures and confirm either way the ralation between the two. (although it certain does sound like thats the case)
You may also try toggling the 'Accurate file system shell icons' option in Preferences>Display>Options to see if this has any effect on the duration of the local directory changing/listing time.
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