I have recently worked on a issue where the customer was experiencing extremely bad performance on a Configuration Manager 2012 R2 site. The backlog for processing status messages was over two hours.
After going over the eventlog, disk performance and other obvious areas the attention was swiched to drivers running in ring 0.
The customer is using (and quite happy with) BitDefender GravityZone – see http://www.bitdefender.com/business/security.html
One of the options that can be enabled in BitDefender is AVC (Active Virus Control). Was we found was that even if the administrator has configured AV exclusions for various processes and files AVC will still examine those.
We disabled AVC on the Configuration Manager servers and found that after a few moments performance started to improve. It still took a few days (!!) before all backlogs were cleared.
The important lesson is that you should consider your AV solutions and optimize it for Configuration Manager.