On the PAL Wizard threshold file tab, when you select the SQL Server 2008 R2 threshold file, does it show that it inherits from System Overview? If not, use the Add button to add the SystemOverview.xml file to it. System Overview should inherit from Quick System Overview (QuickSystemOvervie.xml). If not, select System Overview and add QuickSystemOverview.xml to it. When they shows as inherited, then it should work fine. Also, all changes to inheritance in the threshold files is immediately saved to the file. This means that when you add inheritance it will always inherit unless you remove it at a later point.
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