Hi
I had a similar issue with Syntax Highlighter evolved 3.1.3 and WP 3.3.2.
In my case, I would paste in my C# code using the TinyMCE button and preview it. Everything ok.
I would then update and view site only to see that
<pre class="brush: csharp; gutter: true; first-line: 1">
get’s replaced with just
<pre>
So no scrollbars and readable c# code
AHhhhhhhhhhhhhh!!!!!!!!!!!!!!!
After about 3-4 times of reapplying the syntax highlighter markup ( manually and with the button) I got a bit fed up. So started to investigate
I think it might be related to the After-the-deadline from Jetpack. I have simply enabled it for the first post update only. I am also not doing the preview before I update – tho this probably more paranoia on my part ??
So far everything ok.
Daniel