If you're like me, love bootstrap, and love programming, you may end up with a similar situation to me. This site runs google's code prettifier on top of the twitter bootstrap.  Some styles in the bootstrap clash with prettifying css, which throws off the linenums formatting. This can be fixed by simply adding the following CSS to your site:

ol.linenums {
	margin-left: 0px !important;
	padding-left: 40px !important;
}

Easy!

Edit: This site no longer runs "Google Code Prettify" or "Twitter Bootstrap", though I do still thoroughly recommend them.