This seems a UI issue. When the modified package is installed, the setting is preserved and it makes Reader the default PDF viewer. It does not throw any checkbox to make Reader default viewer at the time of installation (Acrobat was already installed on the system).
If this setting would not have been preserved, it would have thrown a dialog with a checkbox to make Reader default PDF viewer at installation time.
I have this exact same problem but we only have 1 user of Acrobat user so it is not something I will spend the time to verify.
It sure does make you question if the option is holding. Also I what happens if you forget to check this option again once you open the transform up a second time.