I came across the same problem and I had a look at the source code. The directive is deliberately initialised later by using a timeout. In the code there is a comment saying "Initialize the plugin late so that the injected DOM does not disrupt the template compiler".
My solution (you can see it in this jsplunker: http://plnkr.co/edit/fXjDxs?p=preview ) is to set the visibility of the select tag to "hidden".
<select ui-select2 ng-model="....." style="visibility: hidden; ">......
When the component is loaded that tag is replaced with a div. In ui-select2.js I have added a line (line 208) to set its visibility to "visible".
elm.prev().css({"visibility": "visible"});