Regression & unittest fixes

This should fix #116 (regression Gaussian09/BH3_fragment_guess.pop_minimal.log).

I initially wanted also to fix regression Gaussian03/ortho_prod_freq.log but that requires a bit more investigation. That's an ONIOM job, and we need to figure out how to handle those for v1.3 reasonably (currently they break the parse), until we consider parsing fragments (I suppose this qualifies as a specific case).