Why are the spherical and cartesian galactic coordinates in the ATNF Pulsar Catalogue different?
The ATNF Pulsar Catalogue's galactic longitude and latitude are heliocentric,
but the origin of their rectangular coordinates is near the center of our galaxy.

The catalogue documentation,
section 6. Distances, says:


  The Galactocentric coordinate system (XX, YY, ZZ) is right-handed
  with the Sun at (0.0, 8.5 kpc, 0.0)
  and the ZZ axis directed toward the north Galactic pole.


From a heliocentric point of view
(U, V, W)
= (8.5 - YY, XX, ZZ).
Then $\tan{l} = V / U$ and $\tan{b} = W / \sqrt{U^2 + V^2}$
as you'd expect.