Forcing Layer2 to run fixes problems some times.  Below are instructions on how to force layer2 to run.

***UPDATE, You no longer have to remove /usr/local/cpanel/cpanel you can now force a layer2 update
by running /scripts/upcp --force


## INSTRUCTIONS
1. Log into the server via the console or ssh as root.
2. type in 'rm -f /usr/local/cpanel/cpanel' Don't worry this is not going to remove cPanel
3. next type '/scripts/upcp' and voila cPanel will force a Layer2 Update


## FOR YOU TECHIES WHO WANT TO KNOW WHY
The reason the above instructions work is simple.  When upcp is ran it downloads a file from cpanel.  This file can vary depending on what your update preference is set to.  In this example we are going to use 'Stable' as our update preference.  cPanel connects to layer2.cpanel.net and downloads STABLE-installer (ex: layer2.cpanel.net/STABLE-installer).  This file is what does the version checking.  If you look at its source you can see that it checks cPanels version by executing ./usr/local/cpanel/cpanel -v..  So if ./usr/local/cpanel/cpanel. does not exist it can.t get the version and therefore cPanels version does not match and layer2 is ran.  Now I know your asking yourself, "well now every time I run upcp it's going to run layer2", that.s wrong.  The Layer2 installer will replace the cpanel binary and upcp will go back to ignoring layer2 unless there is a new version.