I’m not sure if this is related, but after updating to the nightly last night, i think 3.1-RC4-17453, a lot of my custom queries as well as my ‘wp_nav_menu’ calls are all returning empty arrays.
I apologize for this. I don’t know why i didn’t think to check this first. a few hours after posting and thinking about the issue, this sort of dawned on me.
i’m actually not using any plugins at the moment, but upon trying the twenty-ten theme, the problem was gone. obviously something is breaking this in my theme.