Shortcuts Missing on Desktop and Start Menu

During my testing of Adobe Acrobat XI with 11.0.10 patch applied, I was getting the shortcuts on the desktop and the Start Menu 100% of the time.  I used the Customization Wizard to remove the Forms icon from the desktop and some other security related registry keys.  After pushing out to 5000 Windows 7 64-bit machines, half of them are missing their shortcuts on the desktop and start menu.  If I run a repair on the machine, they come back.  I have not seen any errors in the MSI log files related to shortcut creation.