best not using ftp like the above poster says, scp or sftp is best, but if you must, check the modes being used.
active or passive??
This should give you a clue of what is going on...
Code:
Active FTP :
command : client >1023 -> server 21
data : client >1023 <- server 20
Passive FTP :
command : client >1023 -> server 21
data : client >1023 -> server >1023
Normally it is a firewall issue/ftp connection tracking on the linux box