This question points out that in the book class, as soon as the \backmatter command appears, the chapter numbering ceases to work properly. Thus, one is essentially forced to put the bibliography after the appendices. In principle, I agree with this ordering. However, my university's administration requires that the contents of my thesis appear in the following order:
- Intro and so forth
- Body
- Bibliography
- Appendices
It is causing me a major headache to get the numbering of the appendix chapters to appear at all. Any suggestions for a workaround?

\backmatter. – Werner Aug 30 '14 at 01:26\backmatter; by default the bibliography is not numbered. – egreg Aug 30 '14 at 11:36