I have this problem as well with 3.3.1. The code in the editor re-writes every time.
I have changed to the Twenty Eleven theme and deactivated all plugins. I also removed all plugin directories except for akismet which comes with.
The editor still re-writes the list as follows:
original:
<ul>
<li>item 1</li>
<li>item 2</li>
<ul>
<li>item 2a></li>
<li>item 2b></li>
</ul>
<li>item 3</li>
</ul>
re-written as:
<ul>
<li>item 1</li>
<li>item 2</li>
</ul> <ul>
<li>item 2a></li>
<li>item 2b></li>
</ul>
<li>item 3</li>
Note how the last list item has no opening or closing <ul>