Pubchem, InChI, SMILES, and uniqueness
Unfortunately Pubchem is right, the two structures have the same InChI string and key, since the protonation state is the same in the zwitterion and the neutral form. So the reason for the discrepancy is by design.
I also always thought, InChI was designed for distinguishing between these conformations, but it turns out to just be one of the limitations of the system. The issue is addressed in section 13.2 of the technical FAQ of the InChI trust:


  The different protonation states of the same compound will have InChIKeys differing only by the protonation indicator (unless both states have a number of inserted/removed protons greater than 12; in this case the protonation flag will also be the same, ‘A’).
  This is exemplified below by standard InChIKeys as well as standard InChI strings for neutral, zwitterionic, anionic and cationic states of glycine (note that neutral and zwitterionic states do not differ in the total number of protons so they have the same standard InChI/InChIKey):