This issue is indeed due to a compromise. The compromise is at the root level and a rootkit has been installed. This rootkit will attach to several syscalls within the kernel and begin serving malicious javascript to random web visitors.
This root compromise is not related to cPanel directly, as it has been reported on many different control panels on many different servers. The compromise is at the system level, and only Redhat 4, CentOS 4, and FC6 appear to be vulnerable at this time. We are actively researching this issue and will have an in-depth analysis of current information posted soon.
The easiest way to confirm the compromise is to attempt to make a directory with a numerical name. Run 'mkdir 1' or 'touch 2'. If this fails with an error similar to the errors below, then it's recommended to contact your datacenter, NOC or a qualified admin who can recover the system properly.
Code:
[root\@cpanel ~]# mkdir 1
mkdir: cannot create directory `1': No such file or directory
[root\@cpanel ~]# touch 2
touch: cannot touch `2': No such file or directory