Microsoft has just updated the following KB Article:
Changes to collections take a long time in System Center 2012 R2 Configuration Manager
Symptoms
When you create several nested collections in Microsoft System Center 2012 R2 Configuration Manager, and then you use PowerShell or the Configuration Manager UI to change the collections, it may take as long as 30 minutes to complete the changes.
Note Even if you do not change the membership of the collections (for example, you change only the description), this problem still occurs.