When an Antares Auto-Tune is initially loaded, it detects the sample rate of the sound on the track. If you change the sample rate, or mix down to a different sample rate, the timing might be off, or the key might change.
To avoid this problem, make sure that you mix down using the same sample rate that Auto-Tune originally detected. For example, if you record at 44,100, be sure to mix down to the same sample rate. To see your recording sample rate, click on the File menu, select Preferences and look at the Sound Device preferences.
If you change the sample rate of a recording on a track, be sure to reload Auto-Tune so that it can detect the new sample rate.
If you want to burn a CD with the Antares Auto-Tune plug-in, you will need to set your playback sample rate to 44,100 Hz. The easiest way to do this is to switch to Wave mode in the Preferences. Then re-load your project with Antares Auto-Tune in it and burn the CD.
Please note that this only happens with Antares Auto-Tune and it does not happen with the free auto tune VST plug-in G-Snap. (Included with Mixcraft as of version 5)