I did my Viva and was given the verdict of revise and resubmit in 12 months. This was a shock as I have 4 peer-reviewed papers in my thesis, and my supervisors had told me it met the criteria, however of course it didnt and i was devastated for a few days. The internal examiner in parrticular was unhappy with it, despite having less issues with it the year before at the 18 month review, and despite it not being in his area of expertise at all.

A lot of the comments they gave me make sense. My supervisors encouraged me to follow the phd by publication format, so i had an intro, methods section, then 6 papers, then a conclusion. However my examiners said this format is not acceptable and want a traditional intro, lit review, methods, results chapters, discussion and conclusion.

However,

He had a student some years ago, who tried to publish a paper which created a new methodology. It was not very good, and remains to this day unpublished. It was presented at a postgraduate forum, however the document is not available online. I met with this student after that and he told me he had given up on his ideas, but we discussed how I may go about creating a better approach. Which I did. It then got published and has been quite widely cited in the short time it has been online.

However when i submitted my 18 month report, the examiner really had a problem with this paper as I had not cited the unpublished manuscript of his student. Maybe I should have but it was my first paper, I didn't know. I only addressed the methodologies widely used in the literature and the journal had a limit of 30 references, so there was hardly space for any more, especially an unpublished manuscript. However the examiner accused me of being dishonest, basically said it was academic dishonesty. However, he permitted me to pass to the final stage. He also didn't comment on the structure of my thesis (phd by publication), which he has recently taken such a dislike to.

In my final viva as soon as my external examiner mentioned this chapter, i could see a sly look come across his face. When the external was talking about it, he kept shaking his head. Then he went through the chapter line by line disagreeing with it, saying his students one is better and how i should have used it. I really can't believe he is suggesting i structure my entire thesis around an unpublished and rejected manuscript, which just happens to have him as a co-author. He kept refering to it by its citation, rather than ever saying he was involved or it was his student. Im not sure if the external knows who the author of that paper is.

I am not sure if this chapter was a large part of the decision to give me revise and resubmit, and maybe it would be justified regardless. But I really feel uncomfortable about this and feel that maybe its a conflict of interest.

I was wondering if anyone has any advice. Is this acceptable or should i raise it as an issue?

Today I received the examiners report. its 6 pages and 1 whole page is about his former students unpublished paper. I just feel this is excessive and inappropriate. No one in the discipline would even know that paper.