follow me around the block on this one, it's weird:
create another blendshape that is EXACTLY the "wrong" eye pose you first had (half open), and nothing more. Name this thing "FIX" for the sake of this talkthrough.
Now, "go to bind pose" on the base head and ADD the new "FIX" shape to the blendshape node (you may want to use the options box for deform->blend shape->add and "specify" the bshape node if it gives you grief about adding another shape)
Now, set FIX to -1 (exactly the opposite effect as what it's been doing in all your shapes; it'll probably look REALLY weird, that's ok)
LEAVE that slider at -1. Let me repeat. For the rest of this, LEAVE FIX at -1.
Now, one by one, take each of the other bshape sliders, set it to 1, duplicate the head (copying the mix of whatever shape and -FIX), and then set the slider back to zero, moving on to the next shape, rinse, repeat. Once you've done all the shapes, you'll have a new set of target shapes that are now "fixed". You then delete the old blendshape node/relationship and create a new one using your new shapes. This should not break anything to do with your clusters, etc.
what you're doing is this: creating an "unbroken" shape (EXACTLY the good-twin to the evil-twin that caused this problem in the first place ) and ADDING that into all your broken shapes, thereby removing the problem. You then "bake" the resultant shape by duping the head (in it's bind pose, this time!).
Then you have a new batch of shapes to assign as blendshapes, this time, without the broken influence.
It's complicated, but the problem itself is complicated. I've written some tools to do this (well, most of it) automatically, but as it was done at work, I can't "release" it. I'm sure I'll recreate it at home some day and publish it on my site. Until then, hope the explanation will do!
Take care -J.