Having met the same issue, i searched a bit and kind of find a temp solution:
in the atler switch dialogue, search for "PRC_SORC_DISALLOW_NEWSPELLBOOK" ... it should be set to "0", if you set it to "-1" all Eldritch Theurge's class features start to work BUT when you level up, you don't get to choose new spells via dialogue, as per the new spellbook feature, and after you rest you lose all the old ones/learned newspellbook spells.
any help would be apppreciated >;<