The difference is that the CADO tools compute the size score by integrating in radial coordinates, whereas Msieve starts in radial coordinates and switches to computing the integral in rectangular coordinates. They don't compute the same numbers in general.
Msieve uses the rectangular integral because pol51opt did, and the GGNFS scripts had a table of precomputed 'good' scores to shoot for. Nonetheless, the radial score is more robust for some reason, i.e. it finds a better minimum a lot of the time.
