First off, thanks for the bug report.
Secondly, a few quick clarifications:
1) You can deactivate an ioun stone by using its unique power again (ie. if it is already up). But see the note later about the bug. You can also get them all down quickly by dying
2) Each stone used (regardless of type) requires 3 points of "control".
3) A PCs "control" rating is equal to +1 for each point of intelligence above 9, +1 for every 2 levels of wizard, and +1 for every 4 points of UMD.
The fact that you only need to have this control when activating them is a much exploited 'feature" among my play group. I have no current plans to plug this exploit, as it would be difficult within the limitations of NWN. I am thinking about increasing the cost for each stone to 4 control points though, which would reduce the amount this helps from 4 stones to 3 (max).
And now for the bug...
Bioware, in their shortsightedness, do not give you a way to arbitrarily set the SpellID for an effect. This would be SO useful in so many cases, including this one.
What that means is that there is no way to determine exactly what an effect comes from in these custom cases (they all have SpellID -1). The usual work-around is to check the effects creator. However, in this case the effects creator needs to be the ioun stone item. We can tell the effect is from an ioun stone by checking the tag of the effect creator.
So far so good. The problem arises when you log off and on again. In this case the effects are re-applied, but the old object reference for the creator now points to an invalid object, as all the items are given new IDs when you log on again. This is a general problem with all effects, and most custom systems that do this sort of thing break in this situtation. It is the reason why you can't deactivate those stones anymore (because the effects aren't recognised as belonging to the stone anymore).
The "solution" (if you can call it that) is to remove all of these effects when you log on (in this case, basically de-activating all the stones). But since all these effects have a SpellID of -1, you can't tell which effects you should remove and which you should leave. You also can't just remove all those with an invalid creator, since this will be true of nearly all effects (including spell effects and such).
So unless you can somehow flag certain effects as being from items (and should therefore be removed), you are stuffed. This is what is happening in this case. The ioun stone effects from the previous login have become seperated from their stones, and are not being recognised by the system. This is why you are starting form scratch each time.
"Am I going to fix this", you ask...
The problem is, I thought I already had (a long long time ago).
Basically when I create the effects I also link in an effect with a type of 0 (I think it is a Hit Point Change on Dying effect or something like that, which has no real effect for a player character). Then when you log on it removes all of these effects from the player. Since it is linked to the other effects it should remove them as well.
I tested this when I added it and it seemed to work. Apparently it isn't any more. So I'll have to take another look. BTW, I added an option to the More Actions item to list all the current effects on the player. If you still have all the stones up you might want to run that and see if you have any of the type 0 effects (I think they are reported as "invalid" or somesuch) that are linked to unknown creators. If none of those exist then they have been removed but not the other linked effects. If they do exist, then they aren't being stripped at all.
And also, a way to desactivate them 
