I suspect this is caused by the anti-idle monitor on the site. It doesn't rate those commands very highly so by sending those commands the anti-idle timer isn't reset. Some ftp servers require an actual file transfer to reset the anti-idle timer.
There really isn't much you can do, apart from asking the ftp owner to turn off the anti-idle for your account.
However you may want to try the latest beta of FlashFXP (v3.3 beta 5) will automatically reconnect if the connection is lost during a ftp search.
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