FlashFXP v3.0.1044 is an unsupported beta, so please upgrade to v3.0.1045 final, or the latest public beta (v3.1.12.1075). BTW, the server you are using isn't Serv-U v5 but Serv-U v6
. Now to your real question, it seems FlashFXP has cached your directory listing so flush your directory cache or disable it at all.
(Directory-> Flush directory cache).