Is it possible for a Cpanel account work with the same password and not work with the ftp server? It is strange that i encounter this problem and also when i try to access the site, it gives 404 error instead of listing the directories (which is normal output). And this is not for all accounts, some of them. What can cause that situation?
What does your error_log reads? you can find the source of the problem since some of the sites are not working and work from there.
Do a.... tail -f /usr/local/apache/logs/error_log
This will show the last few lines of your log file, it will show you what happened.
Possible cause...A 404 error usually occurs whenever someone requests a URL that is not on your server. Either they mistype something, or there was a typo link somewhere, or you moved or deleted a document that used to be on your server.
Also open your access_log in a new window to see whether the problem has been fixed after your are done as a check.