Please provide more information like specific OS and version. Also please list the names and versions of the ftp clients that you are using when you experience the problem.
A lot of files in a single directory can cause many programs to have problems. I would recommend reducing the number of files in a folder, by putting them in several folders.
The FTP client that you are using probably has an option to look at the raw log and you should be able to use that to determine if it's a problem with the server or your client. The clients could be using a slightly different method to retrieve the list of files.
The story is in the logs.