There is a weird compatibility issue with the highly popularSyntaxHighlighter Evolved Plugin. You can look at the following post, to see how I'm using it:
Notice the two "code" areas, with line numbers?
SyntaxHighlighter Evolved uses shortcodes, like many other plugins and can be used to identify several programming languages (See: http://en.support.wordpress.com/code/posting-source-code/)
The generic shortcode is:
[sourcecode]your code here[/sourcecode]
When you want to highlight a supported programming language, the shortcode will look something like this:
[sourcecode language="html"]<!-- This site is optimized with the Yoast WordPress SEO plugin v1.2.5 - http://yoast.com/wordpress/seo/ --> <title>Bamajr.com - Internet Marketing, Search Engine Optimization (SEO) and Web Design</title> <link rel="canonical" href="http://bamajr.com/" /> <link rel="next" href="http://bamajr.com/page/2/" /> <!-- / Yoast WordPress SEO plugin. -->[/sourcecode]
I always wait to add this feature, until the very end and noticed the issue yesterday.
Before I added the...
...shortcode, your WordPress SEO plugin, identified my post, with an all GREEN rating.
After adding the code...
[sourcecode]There are 1 words contained in the body copy. This is far too low and should be increased.[/sourcecode]
...turned red and...
[sourcecode]The keyword density is 0%, which is a bit low, the keyword was found 0 times.[/sourcecode]
Both of these values had changed from the GREEN range, to RED and ORANGE after the shortcode was added. If I take the shortcode out, the following line changes back to GREEN...
[sourcecode]The keyword density is 1.40%, which is great, the keyword was found 18 times.[/sourcecode]
...and the line, I identified above, as RED, goes away completely. This, of course, changes the SEO status back to GREEN.
I'm not sure why it is doing this, but I'm sure it isn't a behavior you want to happen.