I thought the spell slots thing might be down to Faiths & Powers, after hearing about a similar issue elsewhere. But if it was, this recent successful bug-free install shouldn't be possible. So, it's a head-scratcher.
But if the bug-free install is the weird one and there is a compatibility issue with the FnP sphere system, then you should be able to solve it easily: addCOPY_EXISTING ~sandrah.cre~ ~override~ // or whatever the NPC .cre name is REMOVE_MEMORIZED_SPELLS BUT_ONLY...to the FnP compatibility code. That will make sure the NPC doesn't have anything "memorized" that isn't actually in her spellbook.
Leveling up might fix it to. Or maybe it's completely unrelated. Dunno. But worth a try. (An upcoming update to FnP will add a scroll to any NPCs so affected that lets them instantly memorize spells without resting - once. So it should be fine even if you set up a divine-class NPC to join and immediately begin a combat.)
REMOVE_MEMORIZED_SPELLS
This is not a good idea. It will remove custom spells from all mod NPCs that come with those without any precaution that they will ever regain them. Or am I mistaken?