Logout confirmation window has been moved to the upper-right corner, skinned to fit in better with other BBB components.
Removed an un-needed commented line
repositioned the logout confirm alert
moved the confirmation box down a little
Merge remote branch 'upstream/master' into skin-logout-confirm
enable the logout confirmation again
Merge pull request #223 from SenecaCDOT-BigBlueButton/skin-logout-confirm

The Alert box skin seems to be working now. I'm not sure why it suddenly started working for me, but I won't question it.