Until ColorCurvature releases his script, here is the correct procedure for what you're trying to do:

(1) export bent limb(s) > you've already done this
(2) using whatever tools you like, fix the deformation on the exported bent limb > you've already done this
(3) here's the tricky part (I was just thinking about what I did wrong last time I tried this, and it's because I didn't do this):
(3a) load the bent limb as a morph target > set it to -1.0
(3b) load the corrected bent limb as a morph target > set it to 1.0
(3c) spawn a morph target from this combination - this will be your joint-correction morph

I was making the same mistake you made, which obviously doesn't work :)