Which protocol is FileZilla using? It only makes sense to compare transfers using the same protocol (and it supports at least one, SCP, which Opus doesn't).
Are the two programs using the same settings?
Is there firewall / antivirus software which may be treating each program differently?
Are there any useful messages in the Opus FTP log? (Detail on how to open the log, and how to put it into Debug mode can be found here.)