I haven't had trouble uploading/downloading anything vis FTP/S or SFTP from my CWP servers, but then I don't think I have any dir approaching 10K-50K contents... which I suppose is not a problem on an XFS filesystem. I would suspect the problem lies with Bugzilla, I mean FileZilla -- as a culprit. Or at least perhaps some setting is your limitation. Have you tried with NcFTP or an alternate client?