I agree with Steve and the
factor!
I find Autopano from Kolor good for mosaicing but it may be more than you're wanting to spend on a product.
The registering issue looks radial and kinda like a tilt or spacing issue. As you are unlikely to have a random spacing issue pop up and tilt would be visible in the individual frames... I'd guess that it is MSICE creating an incorrect distortion map when aligning the frames.