[eluser]jedd[/eluser]
I'm unconvinced that you are getting my point.
My point is that your two queries are not identical. This is evinced by the fact that they return non-identical results.
So, as a way of answering your question, you will first need to establish what is different between the two queries when they hit the database.
The most obvious, and easiest, way of doing this is to insert one line into your controller's constructor, as I suggested, to take advantage of the [url="http://ellislab.com/codeigniter/user-guide/general/profiling.html"]CI Profiler[/url]:
Code:
$this->output->enable_profiler(TRUE);