what you neglected to mention is this is not regular download, but rather site-to-site tranfer.
during FXP(site-to-site), FlashFXP tell one site to connect to another and then await untill both sites say file transfer is ready.
FlashFXP has no control over how fast the transfer is going.
you'll have to figure out which site is slowing down after 1st file and then inform site's admin to correct that problem..
or it's possible that those 2 sites just don't like each other
