You can use the script from your Diagnostic Server machine under Program Files\Dell or Quest Software\Diagnostic Server\agent\conf\Package\sqlserver_spotlight\2005\QS_FragmentationByIndex.sql to execute against monitored instance to get the percentage of fragmentation.
In addition, we plan to change this collection schedule and also enlarge its timeout limit in a future release (enhancement reference number SOSSE5229)
Until then turn off this collection “Fragmentation overview” in Scheduling dialogue against all instances.
Go to Scheduling dialogue to select the problematic connection to disable background collecting against “Fragmentation overview” and then applying this connection configuration into all other problematic sql server connections.
Index Fragmentation collection has been redesigned in the current release of Spotlight on SQL Server Enterprise. Latest version of Spotlight can be downloaded from here.