There was a similar thread, where the problem was a router was timing out the connection after a set amount of time.
If you look i'm sure you'll find it.
There is an experimental option in FlashFXP located in options / preferences / firewall tab / send noops during transfer, checking this options FlashFXP will send a NOOP during transfer to keep the connection from timing out, this option is not compatible with all ftp servers, and may in fact cause problems. WarFTPd is one of these servers that it wont work with.
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