Microsoft has released the following KB article:
Discovery Data Manager slows when it rebuilds .ncf files on startup in System Center 2012 Configuration Manager Service Pack 1
Symptoms:
At primary site servers in a site hierarchy, Discovery Data Manager (DDM) spends significant time rebuilding network configuration data files (.ncf files) for other primary sites and their child sites when Microsoft System Center 2012 Configuration Manager starts. The rebuilding of the .ncf files occurs even when there are no boundary changes that were made since the last time DDM built the .ncf files. This blocks other DDM processing. In most hierarchies, the NCF rebuild operation is quick enough that the work is insignificant. However, when there are many boundaries that are configured for one or more sites, DDM throughput can be affected.
Full details at:
http://support.microsoft.com/kb/2931044