This is actually what you WANT to happen. You want MC to control the output format.
If you think that your DAC does best when fixed at a certain sample rate, you can have MC resample everything to that rate. Like Glynor said, you can control that through the mapping table in Output Format, located inside the DSP Studio. (Player > DSP Studio > Output Format > Sample Rate)
I think the best advice is to let MC play everything at it's native rate as long as your DAC can play those rates. For any sample rate your DAC can't play, tell MC to resample to something your DAC *can* handle.
Brian.