If you start FlashFXP and continue to let it run for say 10min does it ever show up?
The only obvious thing that I can think of is maybe the default download folder is pointing to a network drive, slow device, or folder containing over 10k files.
In that situation it can result in a slow startup of FlashFXP.
To solve the problem the easiest solution would be to locate the FlashFXP.ini typically in %AppData%\FlashFXP\4 or %ProgramData%\flashfxp\4\ and rename the file. If renaming the file resolves the problem, close FlashFXP, then delete the new flashfxp.ini and rename the original back to flashfxp.ini, then open the flashfxp.ini in notepad and find the following values under [main] and delete the whole line and save the file. Start FlashFXP.
Download Directory=
DF1=
DF2=
Another possibility while extremely rare is that when you imported your sites it resulted in duplicate site identification tags, if duplicate site IDs are found then FlashFXP must re-generate the site ID's, this can be a time consuming process if you have 100s of sites.
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