Managing citations reliably, especially using BibTex (from e.g. Zotero)

Question

I am using MMA 10.1 on Win 7 64-bit. I have read various questions lamenting poor/non-existent citation capabilities in MMA.

My experience is that I was able, once, to get some BibTeX citations out of Zotero and into Mathematica using plain BibTeX export.

However, having just exported a new BibTeX file, on trying to add a new citation all previous citations were lost (though the citation references [n] remain) - and the new citation didn't appear either.

I tried using an EndNote formatted export as well, but that couldn't even be read (Does it need the EndNote dll? If so, why - it's XML!)

Question: is there any known combination of formats (e.g. BibTeX, Better BibTeX, etc.), procedures, constraints (e.g. reference only 1 file) that will reliably allow citations to be imported, managed etc.?

How does anybody else manage?

(NB the Citation error 1792 or whatever also crops up and has been reported)

As Requested - Minimal Example(s) and further info. (Indented bibfile lines begin with tabs.

Bib file 1

    @article{schmidt_new_1997,
    title = {A new proof of {Birkhoff}'s theorem},
    url = {http://arxiv.org/abs/gr-qc/9709071},
    urldate = {2014-01-06},
    journal = {arXiv preprint gr-qc/9709071},
    author = {Schmidt, H.-J.},
    year = {1997}
}

Bib file 2

@article{uneyama_fluctuation_2015,
    title = {Fluctuation analysis of time-averaged mean-square displacement for the {Langevin} equation with time-dependent and fluctuating diffusivity},
    volume = {92},
    url = {http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92.032140},
    number = {3},
    urldate = {2016-09-28},
    journal = {Physical Review E},
    author = {Uneyama, Takashi and Miyaguchi, Tomoshige and Akimoto, Takuma},
    year = {2015},
    pages = {032140},
    file = {1411.5165v3.pdf:D\:\\User Julian\\Documents\\Bibtex\\Zotero\\storage\\9X8G6FWP\\1411.5165v3.pdf:application/pdf}
}

@article{schmidt_new_1997,
    title = {A new proof of {Birkhoff}'s theorem},
    url = {http://arxiv.org/abs/gr-qc/9709071},
    urldate = {2014-01-06},
    journal = {arXiv preprint gr-qc/9709071},
    author = {Schmidt, H.-J.},
    year = {1997},
    file = {A new proof of Birkhoff’s theorem (Schmidt, 1997) (9709071v1.pdf:D\:\\User Julian\\Documents\\Bibtex\\Zotero\\storage\\S62IV3MV\\A new proof of Birkhoff’s theorem (Schmidt, 1997) (9709071v1.pdf:application/pdf}
}

Open new notebook; make text cell; insert citation, use bibtex and refer to file 1. Insert the only item. It works.

Create second text cell; insert citation using second bibtex file. 2nd citation appears but 1st disappears, and new citation is numbered 1.

Issue unresolved by rebuidling bibliography.

Use of 2nd bibtex file causes error

INTERNAL SELF-TEST ERROR: EndNoteUtil|c|1782
Click here to find out if this problem is known, and to help improve
the Wolfram System by reporting it to Wolfram Research.

It would seem that the "file" parameter may cause the error, but does that having anything to do with the corruption of the bibliography?

Further info

This bibtex entry (saved as a single file) is read by citation, but as soon as search is clicked for "Boyd" the dialog list is replaced with a MMA formual grid[...] and error message as shown below

@misc{john_r._boyd_destruction_1976,
    title = {Destruction \& {Creation}},
    url = {http://danford.net/boyd/destruction.htm},
    author = {{John R. Boyd}},
    month = sep,
    year = {1976},
    file = {Destruction & Creation (John Boyd).pdf:D\:\\User Julian\\Documents\\Bibtex\\Zotero\\storage\\Z3FXM2D5\\Destruction & Creation (John Boyd).pdf:application/pdf}
}