Hi Marcus,

1) The main reason we constructed the 256 version of the atlas was to make it compatible with DTI-TK, since DTI-TK requires 128x128 or 256x256 images. The 256 and non_256 versions of the IIT v.3 atlas have exactly the same contents. The only difference is in the matrix size. 
2) The non_256 version of the IIT v.3 atlas has 182x218x182 dimensions and is in ICBM152 space. If you would like to use the ICBM-81 white matter labels, you can actually find them in the 182x218x182 matrix size in FSL (look in the fsl/data/atlases/JHU directory). This should fix the issue of the single voxel difference you mentioned.
Also, please note that, very soon, we will be releasing white matter tract labels customized for the IIT v.3 atlas (in 256 as well as in non_256 space). Check back for those soon.

Regards,
Konstantinos