FileZilla cannot display more than 1998 files per folder, but if you use the ls -l | wc –l command in Putty, you will obtain the real file count (x fichiers + 1 link to the parent-folder).
Source: http://forum.filezilla-project.org/viewtopic.php?f=2&t=14688 : The server intentionally cripples the directory listing. In order to “save bandwidth”, some servers truncate listings at exactly 2000 files (1998 files and the two special entries . and ..). That is a decision made my the server, FileZilla can’t do anything about it.