Alert: Troubleshoot-CI.ps1 encountered an unexpected error.

After moving our Exchange 2010 SP3 mailbox servers from a SCOM2007R2 to SCOM2012R2 environment, we are getting the following errors in SCOM for all 12 mailbox servers in 2 different forests.

Alert: Troubleshoot-CI.ps1 encountered an unexpected error.
Source: Mailbox Monitoring - MBX1002 (Mailbox) - Default-First-Site-Name
Path: MBX1002.domain.local;MBX1002 (Mailbox) - Default-First-Site-Name 
Last modified by: System 
Last modified time: 17-6-2014 14:21:09 
Alert description: The troubleshooter failed with exception The troubleshooter failed with error:System.Management.Automation.RuntimeException: Cannot index into a null array.
   at System.Management.Automation.ArrayReferenceNode.GetValue(Object target, Object index, ExecutionContext context)
   at System.Management.Automation.ArrayReferenceNode.Execute(Array input, Pipe outputPipe, ExecutionContext context)
   at System.Management.Automation.ArrayLiteralNode.Execute(Array input, Pipe outputPipe, ExecutionContext context)
   at System.Management.Automation.MethodCallNode.Execute(Array input, Pipe outputPipe, ExecutionContext context)
   at System.Management.Automation.AssignmentStatementNode.Execute(Array input, Pipe outputPipe, ExecutionContext context)
   at System.Management.Automation.StatementListNode.ExecuteStatement(ParseTreeNode statement, Array input, Pipe outputPipe, ArrayList& resultList, ExecutionContext context) 
At C:\Program Files\Microsoft Monitoring Agent\Agent\Health Service State\Monitoring Host Temporary Files 13\2674\CITSLibrary.ps1:1925 char:65+             $message = $message.Replace($substring, $Parameters[ <<<< $i - 1]).
EventSourceName: CI Troubleshooter

error: 

System.Management.Automation.RuntimeException: Cannot index into a null array.

When I run "C:\Program Files\Microsoft\Exchange Server\V14\Scripts\Troubleshoot-CI.ps1" manually on these mailbox servers, it runs without problems. I see other people with the exact same issue, but no real solution has been provided. Hope anyone can help out here.