I don't think there are any limitations of that sort in edtFTPj. Of course, upgrading to the latest version is always advisable. All version are backward compatible.
I suggest logging in with a command-line ftp client, such as ftp.exe on Windows, and doing a file-listing that way. You can then compare the two listings. You could also try using another FTP client application such as FileZilla, which shows the number of files in the status-bar.
- Hans (EDT)