The Partial Color Mode "default" on the NEX-5N seems to be set at the middle tint of the isolation colour of choice (yellow selected below).
Because yellow has various tints and shades (from mango to lemon, light and dark), the software can sometimes miss certain yellows that are outside of the default parameter (left pic).
Click left on the menu wheel to select - Brightness - Colour - Vividness (below the screen, which are all set on Auto default) and customize values to widen the parameter until it encompasses the object's colour entirely before taking the shot (right pic). The controls can also be used to narrow down the parameter further to exclude undesirable yellows if the composition requires it (let's say I just want the top of the pencil sharpener to be yellow).
Same goes for Blue, Red, and Green.
Obviously this shooting mode will work best with simple and clearly defined coloured objects... and can't be expected to excel in overly complex coloured environments.