If you need to create the SharePoint application instance after installing PPS Monitoring, you might need to be sure the following is place in the web.config file for your new SharePoint site:
You should have the following entry in the section of the config file:
<SafeControl Assembly="Microsoft.PerformancePoint.Scorecards.WebParts, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" Namespace="Microsoft.PerformancePoint.Scorecards.WebParts" TypeName="*" Safe="True" />
Once you have added it run IISReset from a command prompt and try your dashboard again.