I can't think of anything which has changed recently and would cause that, so there's probably another factor causing the difference. That might be antivirus or firewall software/hardware, or changes on the server side.
Do you know if their upload tool uses the same type of connection? It may be using another protocol to the one you're using in Opus. (Opus may support the one they are using, depending on what it is.)
What does the FTP log say, and the other things in the FTP FAQ?