Placement of Conditional Styles in Code: fix door Omega

Should the Conditional Styles always show up in the code AFTER the active theme CSS? I'm trying to use this module with the Omega theme, and it seems as though my IE-specific styles are being rendered before the theme CSS, which in effect, seems to make them useless. I'm just trying to track down where this can be fixed, through this module or through Omega. In other themes, it seems to be rendering the right order, so it makes me think it's a theme-specific issue.