I've just had a similar problem with FTP between two gigabit connected boxes which wouldn't transfer at more than 100KB/sec. It took a while but eventually I found that the default BlockSize in Net::FTP is 10240 bytes (compared to a 4096 bytes in the command line FTP.exe) By tweaking the BlockSize, transfer rate changed from 100KB/sec to 2000+KB/sec. The next exercise is to optimise the blocksize for each server we use depending on network, firewalls, throttling etc...
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