I noticed this same behaviour two times till now, with the last releases of FlashFXP available.
I had a queue with mixed upload and download files. And suddenly FlashFXP started to send QUIT after each file successfully uploaded, though the queue was not empty.
The "FTP/On transfer complete" option was set set to "idle".
I can just testify I met the problem but I couldn't get any clue about what had caused this.
FlashfFXP just sent QUIT immediately after having uploaded one file of the queue, that's all the status window was showing.
I restarted FlashfXP and everything worked all right, with the same FTP sites.