http://www.mathjax.org/resources/docs/?//options/hub.html
for details.
As for flushleft, this is a text-mode environment, and MathJax doesn't  
implement them (only the mathematics environments), so that can't be  
used to control the placement of the equations.  The displayAlign and  
displayIndent settings are global to the page, so you can't have  
regions with different settings.  It may be possible to use CSS to  
override it selectively, but I haven't tried that out, and it would  
need to be carefully handled.
Davide
Can you post your configuration settings?  Or a URL to a test page  
that exhibits the problem?  (You can send by email if you prefer not  
to make it public.)
Davide
Davide
On Jan 24, 2011, at 10:49 PM, Nolan wrote:
Note that config/MathJax.js is only loaded when there is no in-line  
configuration.  If you want to load it as well, use
	MathJax.Hub.Config({
            config: ["MathJax.js"],
	   ... (the rest of your configuration here) ...
	});
I see that you are loading the jsMath2jax extension, but that is not  
needed in your case because your page includes the <script> tags  
already (not <span class="math"> or <div class="math"> for jsMath).   
So your configuration could look like
	<script src="http://www.nolanhergert.com/mathjax1.1//MathJax.js">
	MathJax.Hub.Config({
	  jax: ["input/TeX","output/HTML-CSS"],
	  displayAlign: "left",
	  displayIndent: "2em"
	});
	</script>
or you could just use
	<script src="http://www.nolanhergert.com/mathjax1.1//MathJax.js"></ 
script>
and let the config/MathJax.js file dothe configuration.
I'm not sure if the need for install_js.php, since you can just  
include the <script> tag directly.
Anyway, the issue is that the configuration parameters are not  
actually being set.
Davide