So, I have suggested TeXnic Center + MikTeX to a fellow PhD student for use for reports and his PhD thesis. At some point, he needed to write an article, and the simplest thing was to copy a TeXnic Center project and modify all the files in the tps and tpc files - this has worked for me in the past.
Trying to compile it today, the bibliography was not included which caused me (as his first port of call) a bit of a problem, most perplexing is the setup I managed to obtain in the end:
Identical tpc and tps files - where one works as a functional TeXnic Center project and the other one doesn't. Moving the files from the working project to the other results in the broken setup working again. Now I have no idea what could have happened, as the setup is reasonably straightforward.
I have attached the two samples as a 7-zip archive, labelled "broken" and "works"...
In the end the only solution I could offer was to create a new project and copy all the content across, but this still leaves the question as to why it occurred in the first place, and this gave a correctly compiling document.
I would appreciate any help in this matter - many thanks.