This is really strange. I don't suppose you have disk based logging enabled? I would be very interested in seeing the last few lines from the status log prior to FlashFXP locking up. Also is there an errorlog.txt in the FlashFXP folder?
After rebooting did the problem continue to occur?
I just an upload of roughly 800 files small files to two different ftp servers and neither queue encountered any problems.
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