I hate to say it, but this bug is serious enough to make me switch syntax highlighters. Anytime I post HTML, XML, XAML, or any other language that uses the less-than/greater-than signs or double quotes, I have to go in and manually edit all of those code samples again directly on the WordPress site in Text mode. Looks like this product hasn’t seen an update in 9 months. I hope it’s not dead, as I really like SyntaxHighlighter Evolved 🙁
I am having the same issue too when posting code from Windows Live Writer using the Source Code Highlighter Plugin for WordPress.com plugin (http://richhewlett.com/wlwsourcecodeplugin/). This worked fine in the past, and only recently started converting things like double quotes to "&. Solution for me to use edit the post in the WordPress editor right on the site and convert the characters back to what they should be.