Upgraded apache when I saw the message in WHM as well and got the same issues like everybody else about the broken links for /cpanel and /webmail
and after waiting for a new STABLE release I had two choices to fix this problem .
Upgrade to an unstable EDGE release ( which seems to bring even more problems ) or just disable suexec .
So i just disabled suexec and the links are all working fine again .
Any feed back from you guys regarding disabling suexec ?