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Thanks for that tip,
I looked at the differences and found that \usepackage[numbers]{natbib} was the cluprate. Without that everything is fine.
So in LyX I set my bib to default (numerical) and everything is right in the world. Thanks for the help! The Natbib was a suggestion from the Wiki, I ...

I don't think so, In the .tex example there's only one REFERENCE section and it was put at the end. I've use the latex command that they use in the example but all that does it put REFERENCE on a separate page then new page chapter x REFERENCE <my references>. See attached.

I guess the big ...

Appreciate your reply Scottkosty, I did indeed read the link and what I provided seemed to be what I needed to produce. If I misinterpreted the intent I apologize. I felt since I was using a special class that I should include it and I removed everything from the preamble whilst still producing the ...

Thanks for trying. I'm not sure about the option "round", I looked and didn't see any reference in the lyx file for round in Natbib. I have it setup for Numerical with the option Alpha (same as the thesis_example).

Fair request. It wasn't hard I already had an example .lyx file ready just needed to add the bib stuff.
Attached a 7z which includes all the required files, I also included the original example .tex file which the lyx template was derived from (where bibtex works).

Greetings!
I'm using Lyx 2.1.4 and I have a custom class generated by my school I'm using to write my Thesis. I'm using JabRef to build my .bib (not important for this question but FYI). I'm using the built-in citation and bib creation (insert-> List/TOC ->BibTeX Bibliography) and everything works ...