most likely what happens is during long transfers there is no activity on control connection, so after a while, in your case "less than 20 - 25 minutes", your router closes that connection, transfer complets normaly, but you don't get 226 becuase control connection is closed, not becuase server booted you out(server knows that there is a transfer, but your router doesn't) and after that flashfxp waits 30sec at which point you actualy see timeout message.
"send noop during transfer" will keep control connection alive..by sending 'noop' during transfer
. like i stated above, this option may cuase problems with some servers.
alternatively you might want to look into your router config and set connection timeout to even larger value.