I think I spoke too soon. She continues to make the funny sharp noise at intervals, and gives her beak/head a sharp shake sometimes. I have had a feel of her crop this afternoon and it was fairly empty, looked in her mouth which was clean and pale pink, the little closey over bit was opening and closing nicely. Whilst I was holding her she kept her beak open, but when I put her down it seemed to close okay. She pecks about fine and dandy and doesn't seem depressed or distressed in any way.
The symptoms aren't typical I know but might it be gapeworm?