You only need to set it in one place, just make sure that you use the "full path" to the file, not relative path. Same goes for TM_LATEX_BIB. Btw, if you bib file is loaded via \bibliography{} into either the master file or a file included in it, then the citation command should be able to find it by itself, you shouldn't set TM_LATEX_BIB at all.
So, this is what I tried and it worked just fine for me:
Structure:
top folder
- "main" folder
- ab.tex
- test.bib
- "includes" folder
- other.tex
ab.tex is the main file. It contains:
\include{../includes/other.tex} \bibliography{test.bib}
TM_LATEX_MASTER is set to the full filepath to ab.tex, which in my case is something like: /Users/haris/Desktop/testing/9_Appendix/main/ ab.tex In this setting, the citation command seems to work just fine for me. Does a similar setting work for you?
I set up a similar environment with the same folder structure, but it again only works with citation inclusion in the main document. I deleted the overall TM shell variable (TM_LATEX_MASTER), it is now only set the (absolute, as before: /Users/n00by/Desktop/title/main/untitled.tex) path is now "project specific". I also deleted the TM_LATEX_BIB variable, as the bibliography is loaded via \bibliography{} in the main document. The only difference is that I have to use \input and not \include for including my chapters, but as I read earlier, this shouldn't be the problem.
I don't know where the problem could be. Maybe i can send you my example-files? Just an idea...