How do I add an iframe whitelist to OS X Server 3.1.1
There is a fix to this problem --
Instead of changing the white list file in /Library/Server/Wiki/Config you have to change the whitelist.plist.default fine in the Server.app bundle (/Applications/Server.app/Contents/ServerRoot/private/etc/collabd/whitelist.plist.default). I did and all works well, even after restart.

Hope that helps!

-Matt

From over on https://discussions.apple.com/message/25866041#25866041#25866041