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I know that double newlines in code blocks are know included in the code, but double new 
lines at the end of the code are included.

example:

* blah, blah. some code:
 do_something_here();

* the above line is included in the code.

As indicated, line 3 is included in the code block.

Assuming I understand the description of the problem, I can't reproduce it at
http://meta.wikimedia.org/wiki/Sandbox/641

Produced HTML is:
<ul>
<li>blah, blah. some code:</li>
</ul>
<pre>
do_something_here();
</pre>
<ul>
<li>the above line is included in the code.</li>
</ul>

which appears correct to me. Resolving as WORKSFORME.