I've been using Otto's plugin since he released it to generate my shortlinks. On upgrade to 3.5, it crashed on me. So I tried your plugin.
It installs perfectly, and works great on new posts. On my test post here
The shortlink was made, and displays when I call for it
But I'm not getting any of my existing shortlinks showing up for any previous posts, they come up as:
<input type='text' value='<?php echo wp_get_shortlink(get_the_ID()); ?>' onclick='this.focus(); this.select();' />
to spit out the shortlink