This is most likely a limitation of your FTP server.
Your FTP server (like many other software) is probably using Windows API functions in a way that limits the maximum path length to 260 characters (see this MSDN article for details) and when Rebex FTP asks it to send a directory listing for a path that is too long, it rejects the request. On the other hand, Windows Explorer is using API calls in a way that makes it possible to handle paths of up to 32767 characters.
To make sure this explanation is correct, please create a communication log using Ftp object's LogWriter property (see this article for details) and post it here or mail it to us for analysis.