You can replicate this issue like this:
- Create a cleric/thief in BGII.
- Use console commands to add 8 million XP. Level up.
- Add one of each high-level ability.
- Click on innate abilities and check if you have all the abilities.
Some innate abilities will not appear in the list. It seems that Cleric/Thieves with a high number of innate abilities will have this issue. I suspect it's because of the Thieving button within Innate Abilities messing with that.
The abilities that disappeared will reappear after you use a few of the other usable abilities.
I thought I found a workaround, when I added another innate ability that started with the Z letter (I thought it had something to do with the name of the abilities), using EEKeeper. That ability that I added didn't appear in innate abilities, but the one that disappeared before doing that, reappeared. However in later levels when another innate ability was added to my character, the one that I added reappeared again, and the one that was added did not appear.
So yeah, something is wrong with the Thieving button there, it seems at least ONE innate ability will not appear in the list.