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Ok I think I've fixed this, kinda. I can get .bbl files from my own .bib files now, provided that the .bib file is in the same file as my .tex file (thanks joseph) and the .tex file hasn't been compiled incorrectly once. If it fails to compile properly once and an empty or invalid .bbl is created ...

Hello. I am a new user to BiBTeX and I am getting frustrated after a day of troubleshooting.

I have the protext MikTex 2.9 + TeXMaker X package configured with bibtex command "bibtex %" and build command "latex -interaction=nonstopmode %.tex|bibtex %.aux|latex -interaction=nonstopmode %.tex|latex ...