The ABOR command is being sent by the client before the 426 response from the server. Which does suggest that it is comming from the client side. Are you using you're Filezilla client from the same machine that your script is running from? Could be a rule on a router or firewall somewhere impacting the script that does not impact your desktop...
Thanks for your help. I couldn't figure out what the problem was with timeout, instead used restart() from FTP::Net to append to the file if the file size isn't correct.