Just an update to the first of these issues - this only seems to be the case 
when I select "Jones Rainbow" using the 
change_model_molecule_representation_mode() function, which I bind to keys as 
below so that I can quickly cycle between representation options without having 
to go to the display manager (helpful when there is a long list of open 
models). 

Once I have selected Jones rainbow once using this method, however, it displays 
the previously described behavior (regardless whether via Display Manager or 
otherwise) until I close the model.

This is all on Mac 10.9.5, using r5399.

Cheers,
Oliver.

Key bindings:
add_key_binding("Cycle representation mode forward","[",
lambda: change_model_molecule_representation_mode(1))

add_key_binding("Cycle representation mode back","]",
lambda: change_model_molecule_representation_mode(-1))

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