I eventually stumbled on the solution to my problem:

I restructured my document removing the #+BIBLIOGRAPHY: bib-file style statement which no longer seems to work, placing the LateX commands to specify the bibliography at the end of the file:

#+LATEX_CLASS: article
#+LATEX_HEADER: \usepackage[margin=0.5in]{geometry}
#+LaTeX_CLASS_OPTIONS: [12pt]

* Objectives
* Stroke care guidelines

#+LATEX: \bibliographystyle{vancouver}
#+LATEX: \bibliography{stroke}

I have this in .emacs to ensure the triple compilation required:
(setq org-latex-pdf-process '("latexmk -pdflatex='pdflatex -interaction nonstopmode' -pdf -bibtex -f %f”))

I have not been able to find any guidance on how to deal with this change in behaviour by org-mode so post this for others to save them the many hours I wasted when I have a deadline to meet


> On 27/06/2016, at 23:20, David Abernethy <david.abernethy@icloud.com> wrote:
> 
> 
> I am exporting a file stroke.org <http://stroke.org/> using the bibliography file stroke.bib in the same directory
> The citations are not being incorporated into the pdf file
> 
> An example from stroke.log: LaTeX Warning: Citation `Drummond:2014aa' on page 2 undefined on input line 71.
> 
> The header for stroke.org <http://stroke.org/> is:
> #+LATEX_CLASS: article
> #+BIBLIOGRAPHY: stroke vancouver option:-d
>