Upgrading to R2 stuck on "Configuration Manager has detected an active MP Replica on this site."

Hello Everyone,
We are installing upgrading our SCCM 2012 server to R2 and we are stuck on;
"Configuration Manager has detected an active MP Replica on this site. Please deactivate this MP before continuing upgrade."
I have tried disabling SQL service on the MPs but that didn't work. So could anyone give me any help on the procedure on how to deactivate the MP as requested?
Thank you in advance for anyhelp.

From the beginning we didn't have Replicas at all! 
We checked each DP and Secondary Site and they are already all disabled.
You should have mentioned that fact earlier ....
What did you check and what's disabled? 
Torsten Meringer | http://www.mssccmfaq.de

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    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:23.685+240><thread=6092 (0x17CC)>
    Sleep 30 minutes... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:26.886+240><thread=2936 (0xB78)>
    ~Used 0 out of 3 allowed processing threads. 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:27.948+240><thread=4900 (0x1324)>
    ~Sleep 3600 seconds... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:27.950+240><thread=4900 (0x1324)>
    Sleep 30 minutes... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:31.934+240><thread=2936 (0xB78)>
    ~Used 0 out of 3 allowed processing threads. 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:33.021+240><thread=4900 (0x1324)>
    ~Sleep 3600 seconds... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:33.023+240><thread=4900 (0x1324)>
    ~Used 0 out of 3 allowed processing threads. 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:38.108+240><thread=4900 (0x1324)>
    ~Sleep 3600 seconds... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:00:38.111+240><thread=4900 (0x1324)>
    Sleeping for 60 minutes before content cleanup task starts.~ 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:06:28.094+240><thread=4968 (0x1368)>
    Sleep 30 minutes... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 16:30:52.271+240><thread=2936 (0xB78)>
    Sleep 30 minutes... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 17:01:10.002+240><thread=2936 (0xB78)>
    ~Used 0 out of 3 allowed processing threads. 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 17:01:10.977+240><thread=4900 (0x1324)>
    ~Sleep 3600 seconds... 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 17:01:10.979+240><thread=4900 (0x1324)>
    Sleeping for 60 minutes before content cleanup task starts.~ 
    $$<SMS_DISTRIBUTION_MANAGER><03-17-2014 17:06:55.337+240><thread=4968 (0x1368)>
    Issue 2: I'm trying to deploy a couple of Packages/Applications using SCCM 2012 R2 running on Win2K8 R2 with no luck, knowing that I could install the packages
    on a test VM “in the DataCenter site”, but when trying to deploy the packages to production PC “in the Office Site”,
     the status is packages deployment compliance stuck at 0%
    Infrastructure:
    3 SCCM servers: CAS, PRI & SEC. Both CAS and PRI are in the DataCenter site, and SEC is in the Office site. The office site has several IP subnets.
    Boundaries are configured through Forest Discovery “IP Ranges and AD Sites” since that the AD site should contain all the IP subnets that the AD site contains, Boundaries groups are also configured and a site reference
    server is configured for each group respectively.
    A OU based Collection has been configured that contains 13 PC "the collection contains the PCs that the packages should be installed.
    Packages/Applications are configured correctly since that I could successfully deploy the packages to the test VM which is on the same subnet as the CAS and the PRI servers "the DataCenter subnet". The issue
    is that I can't deploy the packages to production PCs in the Office subnet!
    Firewall rules are configured and applied via GP, and I even turned Windows Firewall off, and still nothing! I tried to manually initiate Computer Policy download via the SCCM GUI and via a script, still no luck!
    I tried configuring IP Subnet Boundaries, still no luck!!
    Here are the last 2 lines in the LocationServices.log of a client PC at the Office Site:
    <![LOG[MPLIST requests are throttled for 00:00:44]LOG]!><time="14:47:00.766+240" date="03-17-2014" component="LocationServices" context="" type="2" thread="5776"
    file="lssecurity.cpp:4528"> <![LOG[Current AD site of machine is Default-First-Site-Name]LOG]!><time="14:47:00.777+240" date="03-17-2014" component="LocationServices" context="" type="1"
    thread="4884" file="lsad.cpp:770">
    And here are the last 4 lines in the ClientLocation.log
    <![LOG[Rotating assigned management point, new management point [1] is: BBK-SCCM-PRI.bbk2310.com (7958) with capabilities: <Capabilities SchemaVersion="1.0"><Property Name="SSLState"
    Value="0"/></Capabilities>]LOG]!><time="14:49:04.880+240" date="03-17-2014" component="ClientLocation" context="" type="1" thread="3600" file="lsad.cpp:6311">
    <![LOG[Assigned MP changed from <BBK-SCCM-PRI.bbk2310.com> to <BBK-SCCM-PRI.bbk2310.com>.]LOG]!><time="14:49:04.891+240" date="03-17-2014" component="ClientLocation" context="" type="1"
    thread="3600" file="lsad.cpp:1532"> <![LOG[Rotating proxy management point, new management point [1] is: BBK-SCCM-SEC.bbk2310.com (7958) with capabilities: <Capabilities SchemaVersion="1.0"><Property Name="SSLState"
    Value="0"/></Capabilities>]LOG]!><time="14:49:05.345+240" date="03-17-2014" component="ClientLocation" context="" type="1" thread="3600" file="lsad.cpp:6374">
    <![LOG[Rotating local management point, new management point [1] is: BBK-SCCM-SEC.bbk2310.com (7958) with capabilities: <Capabilities SchemaVersion="1.0"><Property Name="SSLState" Value="0"/></Capabilities>]LOG]!><time="14:49:05.786+240"
    date="03-17-2014" component="ClientLocation" context="" type="1" thread="3600" file="lsad.cpp:6436">
    It looks like clients in the Office Site can’t connect to the DP/MP of the Secondary Site server which is also a DP.
    While on the PC that the application was installed on I see the folowing in the LocationService.log:
    <![LOG[Distribution Point='http://BBK-SCCM-PRI.bbk2310.com/SMS_DP_SMSPKG$/Content_69547d2a-339f-4ac4-9523-238c79ff8a52.1', Locality='LOCAL', DPType='SERVER', Version='7958', Capabilities='<Capabilities SchemaVersion="1.0"><Property
    Name="SSLState" Value="0"/></Capabilities>', Signature='http://BBK-SCCM-PRI.bbk2310.com/SMS_DP_SMSSIG$/Content_69547d2a-339f-4ac4-9523-238c79ff8a52.1.tar', ForestTrust='TRUE',]LOG]!><time="14:42:59.506+240"
    date="03-17-2014" component="LocationServices" context="" type="1" thread="224" file="lsutils.cpp:415"> <![LOG[Calling back with locations for location request {144620BC-4BF0-4878-9554-F67D305ECCF8}]LOG]!><time="14:42:59.522+240"
    date="03-17-2014" component="LocationServices" context="" type="1" thread="224" file="replylocationsendpoint.cpp:220">
    Is there something wrong with the Distribution point on the Secondary Site server?
    Please help…
    Thanks..

    Update:
    I fixed the issue with the default XXX00002 package - "Configuration Manager Client Package", it will not deploy to the Secondary Site DP. I did that through "Update Distribution Points" option, and after a while the status was 100%.
    However; the second issue is still unsolved...
    Please help..

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