Somehow I have become seriously confused. Either I got totally lost in this thread or someone merged two threads or something.
At any rate.
Does this problem occur on a single ftp sever or multiple servers? When you said you tested with your university, I thought you meant their ftp server.
You said you were using 3.5.1, did you have this problem with the 3.4 stable release?
Does it help if you enable "Send noops during trasnsfer", You can enable this option Globally via the Preferences / Proxy Section or Per-Site in the Site Manager.
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