Based on your log I have a couple questions.
1. Are you using the following option (Pref/Proxy Tab/Limit Local Port Range) ?
2. Do you have a firewall? Some firewalls will detect the many incoming connections (PORT) as a port scan and start rejecting connections for a few seconds before allowing them again.
3. Which FTP server software is the server running?
Now that I fully understand what's going on, I will conduct some tests and see if I can reproduce/determine the problem.
There is one test you can help with, try another ftp client and see if you encounter the same problem. If you do then we know it's the FTP server and will save us all alot of time.
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