Hello MT,
Version 1 instruments have no pitch information either in the samples or within the organ definition file, so by default this option is deliberatly disabled since it cannot work without the proper pitch information of the original samples. Hauptwerk v 1 had no facility for specifying pitch of the samples which is required in order to change temperaments accurately.
All version 2 instruments and beyond generally have this information included so unless the producer specifically disables the temperament options you can use a native Hauptwerk 2/3 instrument and temperaments will be available.
Thus there is nothing wrong since that is intended.