In the Convert pane at the lower left, you'll see Options. Click that and you'll get a big dialog box. Near the bottom center of that dialog is a part that says "Apply DSP..." and a clickable link that for DSP Settings. If Apply DSP is checked, then the DSP settings will get used, including and Output Format settings that you have set up.
If that's not it, try to convert to a different format like ALAC or something else that can contain 24/96 audio.
Good luck.
Brian.