On uninstall Msi executes setup.exe
Autoupdates needs to be disabled
Resolutions and key notes :-
Custom Action RIM_MSIUsedForInstall has been commented Since this custom action calls the setup.exe for the installation of the application .While we need to install the application from the MSI.
Registry value has been changed to HKEY_CURRENT_USER\Software\Research In Motion\DesktopAutoUpdate\
"AutoUpdateEnabled"=False to disable the automatic updates.