The only difference between the files is the resolution, the downloadable files have half a degree resolution while the webrun files have a quarter of a degree. This is deliberate, because the underlying resolution of the LAB gas survey is around half a degree.
You should get the exact same results from webrun and the downloadable code if you use the same spatial resolution and CAR projection output from GALPROP. The HEALPix option will be only slightly different because the pixel boundaries do not match between the output and the input.

_________________
Gudlaugur Johannesson, GALPROP developer

I did not say the numbers aren't significant, only that the differences between the files in webrun and those distributed with the code is the resolution. And there is not a one-to-one correlation between the version numbers of the HI and CO files, they are just bumped up when we make changes to the files, some of which are never released.
CAR is plate carrée projection. It is used unless healpix output is selected.

_________________
Gudlaugur Johannesson, GALPROP developer