Microsoft has just updated the following KB Article which applies to ConfigMgr 2012:
The SMS Discovery Data Manager component may take a long time to process discovery data records after the component starts
Symptoms:
In a large Microsoft Systems Management Server (SMS) hierarchy, the SMS Discovery Data Manager (DDM) component may appear to pause for a long time after the component starts. The delay may cause a backlog of discovery data record (.ddr) files.
Full details at:
https://support.microsoft.com/en-us/kb/838655