Hi there,
the answer may be a little late but... if you are using the repackager or aac youve to set the following variable in the repackager folder\default.ini:
C:\Program Files (x86)\AdminStudio\11.0\Repackager\default.ini
CheckDeletedRegistry=0 to 1
Otherwise you can manual edit your msi package with the editor ;-).
Regards
Thomas