I personally prefer to set biblatex's package options in a .bbx file using \ExecuteBibliographyOptions so that I can just call biblatex minimally in my preamble (preferably using only \usepackage[style=myStyle, natbib=true,backend=biber]{biblatex}). I noticed however that some options do not work when parsed from the .bbx file using \ExecuteBibliographyOptions but must be supplied in the preamble using either \usepackage options or \ExecuteBibliographyOptions. In my case I found the following options to cause the problem while others worked fine:
- labelyear
- uniquename
- uniquelist
Of course, I only use a small set of all the possible options so there very well be more options with the same problem.
EDIT - added minimal example
Calling for options from an external .bbx file
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{mystyle.bbx}
% Build on the original author-year comp
\RequireBibliographyStyle{authoryear-comp}
\ExecuteBibliographyOptions{
maxcitenames = 2,
mincitenames = 1,
firstinits = true,
terseinits = false,
labelyear=true,
uniquename=false,
uniquelist=false,
}
\end{filecontents}
\begin{filecontents}{mystyle.cbx}
\ProvidesFile{emi.cbx}[biblatex style for Environmental Microbiology]
\RequireCitationStyle{authoryear-comp}
\endinput
\end{filecontents}
\begin{filecontents}{\jobname.bib}
@article{ref1,
author = {Doe, J. and Dane, D., and Dewy, R.},
year = {2000},
title = {This and that},
journal = {Journal of deep understanding of things},
}
@article{ref2,
author = {Doe, J. and Dewy, D., and Dane, R.},
year = {2000},
title = {The other},
journal = {Journal of deep understanding of things},
}
\end{filecontents}
\usepackage[style=mystyle,natbib=true,backend=biber]{biblatex}
\addbibresource{\jobname.bib}
\begin{document}
Some text and a ref \citep{ref1}.
Then another ref with same first author and year \citep{ref2}
\printbibliography
\end{document}
Produces an undesired output:

But calling for the same options with \usepackage produces the desired output
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{\jobname.bib}
@article{ref1,
author = {Doe, J. and Dane, D., and Dewy, R.},
year = {2000},
title = {This and that},
journal = {Journal of deep understanding of things},
}
@article{ref2,
author = {Doe, J. and Dewy, D., and Dane, R.},
year = {2000},
title = {The other},
journal = {Journal of deep understanding of things},
}
\end{filecontents}
\usepackage[style=authoryear-comp,natbib=true,
maxcitenames = 2,
mincitenames = 1,
firstinits = true,
labelyear=true,
uniquename=false,
uniquelist=false,
terseinits = false,
backend=biber]{biblatex}
\addbibresource{\jobname.bib}
\begin{document}
Some text and a ref \citep{ref1}.
Then another ref with same first author and year \citep{ref2}
\printbibliography
\end{document}

\ExecuteBibliographyOptions. You'll have to demonstrate your problem. The options you mention are set in some of the standard styles without issue. – Audrey Nov 25 '12 at 03:30backendshould also be in that list. Could've sworn we already made that edit to the manual... – Audrey Nov 25 '12 at 17:06