SQL SERVER 2008 Database went into recovery mode and Change tracking is throwing errors. Already installed hot fix/ CU

Not sure if this is the correct forum but here goes.

Good Day All,

My name is Julian and I am a dba. Recently we had an issue on our reporting server that required us to bounce the sql server services. Once we did that, there were several databases that went in recovery mode. Once they came back up we started receiving some errors in our logs.  Here is the error:

The messages are shown below in context (if applicable):           

Warning              11/21/2013 8:09:37 AM  spid14sError: 2601, Severity: 14, State: 1.

OK          11/21/2013 8:09:37 AM spid14sCannot insert duplicate key row in object 'sys.syscommittab' with unique index 'si_xdes_id'. The duplicate key value is (4159095315).

Warning              11/21/2013 8:09:37 AM  spid14sError: 3999, Severity: 17, State: 1.

OK          11/21/2013 8:09:37 AM spid14sFailed to flush the commit table to disk in dbid 20 due to error 2601. Check the errorlog for more information.

After some research we found out that there was a bug that caused an issue with a database that goes into recovery mode that has change tracking enabled. We tried the suggested method proposed by Microsoft(apply hot fix, etc..)  with no luck. So we did the hot fix disabled change tracking and turned change tracking back on. We are still receiving the error on three db containers. Below is the topology:

1. We have our production OLTP server that has a two node cluster(active/passive). Version: Microsoft SQL Server 2008 (SP1) - 10.0.2531.0 (Intel X86)  Mar 29 2009 10:27:29   Copyright (c) 1988-2008 Microsoft Corporation Enterprise Edition on Windows NT 6.0 <X86> (Build 6002: Service Pack 2) (VM)
2. We have our production Reporting server that also has a two node cluster(active/passive). Version: Microsoft SQL Server 2008 (SP3) - 10.0.5844.0 (X64)  Jun 26 2013 22:58:48   Copyright (c) 1988-2008 Microsoft Corporation Enterprise Edition (64-bit) on Windows NT 6.1 <X64> (Build 7600: ) (VM)
3. The OLTP server replicates several database containers to our Reporting server.
4. On the replicated copies that live on our production Reporting server, we have change tracking turned on for the data warehouse. This is the server with the issues above.

I have done some research and found a couple of other methods, however they are pretty serious and will require down time plus we don’t know if that fix would work. So I am reaching out to find out if anyone has had this issue after the hot fix and how you resolved the issue.

Thank you for your help

Julian