Use /qb or /qn switch instead along with your transform (wherein you have disabled updates) e.g.
msiexec /i AdbeRdr11000_en_US.msi TRANSFORMS=<some_name.mst> /qb
or
msiexec /i AdbeRdr11000_en_US.msi TRANSFORMS=<some_name.mst> /qn
It will not alter any settings for the updater preference (The one, which is seen in the Installer Setup dialog)
Alternatively,
If you still don't want to use /qb or /qn switch, you can continue with the installation,
FeatureLockDown key takes the precedence and it will override any updater preference.
And so you can continue Reader with disabled updates.
Tip:
If you are using Customization wizard to disbale update, there's a small check box under,
Online Services and Features > Disable product updates check box.
This does the same as manually adding the FeatureLockDown Registry Key.
Hope, it helps.