In layman's terms, flashfxp can only do one thing at a time within that one session. The server is simply passing the message on through the same text-layer as it uses for the normal text-messages that accompany a transfer.
Notice how you are able to navigate the tree-view that covers your local files while the remote-view is locked while it is executing a command? The client would have to use a separate thread to interact with the server while eg. a transfer is underway.
You could always use another instance (F12), but it would obviously require another login.
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