Islands originally sheltering a large flightless bird (5).
S - M - A
This always looked like SAMOA but I had to look up flightless birds to discover there was one called a MOA, now extinct.
I've finished the crossword now but there is one I still can't quite figure out.
Fruit father always rejected (6).
P - - - Y -
I've got PAPAYA. It's a fruit and PAPA is father but I don't see the "always rejected".