Why does the dipole moment of molecules go from positive to negative?
You have assessed the problem correctly. Physicists and chemists use just the opposite directions. Keep in mind that both are arbitrary choices, however the physicist's convention is consistent with electrostatics. All you have to do is to be aware of this direction in the chemistry literature. I have rarely seen any student ever thinking about it which is rather sad.

If you want more details read this article Misconceptions in Sign Conventions: Flipping the Electric Dipole Moment


  "Most chemists draw the direction of an electric dipole backwards. This inconsistency in sign convention is more than a trivial oversight or matter of convenience. We are introducing an incorrect convention that is central to our student’s understanding of fundamental thermodynamics; which way is up? As a student matures from general chemistry to organic through analytical, physical, inorganic, and biochemistry they are reintroduced to similar, powerful concepts that hold our discipline together. However, this reconnection of chemical principles comes with each subdiscipline’s own idiosyncrasies and a highly contextual framework. Reexamination of a central concept from the perspective of a new subdiscipline should not introduce misconceptions about that concept. When misconceptions introduced through chemical language can be avoided, we should change the way we speak."