I've also got the same problem I think, see the support ticket I've filled for the subdomains I've noticed it occuring on.
On the subdomains affected the CSS isn't loading (I did noticed they used @import). Similarly graphics aren't loading, the paths are fine however trying to enter the path as a URL results in being redirected back to the root of that subdomain. I've checked the htaccess files and they haven't been touched for days. The problem occured just over an hour ago for me, based on a chat I had with someone in the USA whom had been using the
website hosting.
EDIT thought: Is Cpanel using auto-updates? As if it's automatically getting and installing the updates that might explain why once fixed the first time it re-occcured.