Adobe Customization Wizard X issue PDF icon and disable display in browser after installation

I have used the Adobe Customization Wizard X wizard to setup a .MTS files for the custom install. When this is installed using SCCM 2012 with command (msiexec /q /i "\\Server\Share\AcroRead.msi" TRANSFORMS="\\Server\Share\AcroRead.mst") this all works fine but all PDFs on the machine that gets this deployment (Windows 7 x64 or Windows XP x86) the icons for the .pdf don't show the Adobe icon they show the generic Windows icon when the program is not assigned but still work to launch Adobe reader. I have tried to unistall and reinstall but still the same resaults. If I install the .msi with no .mst the icon shows up just fine. So it has to be something with when you use the customization wizard or the .mst. I have also tried assigning .PDF to another program and the icon changes to that program and assign it back and no icon. Also if I set Display PDF in browser = Disabled this setting does not stick. I have just installed via Adobe not using SCCM via command line I get the same resaults.
I have only selected these customizations:
     Installation Options:
Silently (No interface)
Suppress reboot
     Shortcuts
No desktop Icon
       EULA
Suppress display of End User License Agreement (EULA)
     Online Features
Disable all updates
Disable Help > Purchases Adobe Acrobat
Disable Product Improvement Program
Display PDF in browser = Disabled
Disabled  All Acrobat.com access

Hi Ben,
Here's what I am trying to accomplish I had Acrobat Standard v10.1.4 scripted so I can deploy it to a Citrix Server (XENAPP6) via SCCM 2007 I have at least 50 licenses of Acrobat Standard deployed to 50 users. All of our Citrix Servers have Adobe Reader v10.* installed as our default pdf viewer. There are other apps that are deployed to this Citrix Server and I wanted to make sure that pdf files open on Adobe Reader instead of Acrobat Standard.
I had to change the installer tables directly so I don't have to get it re-scripted to use this command line. Is it a best practice not to change the isntaller table?
msiexec /i "\\source\Acrobat10\AcroStan.msi" transforms="\\source\Acrobat10\AcroStan.mst" LEAVE_PDFOWNERSHIP=”YES” /qb /norestart
Thanks a lot for your help I'm looking forward to hear from you.
Regards,
William

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