Hello,
Thank you for contacting National Instruments. Autotune works well for most systems given the axis parameters are configured properly. In cases where Autotune doesn't seem to work properly you'll need to manually tune the motor. See the following tutorial regarding information on manual tuning: http://zone.ni.com/devzone/conceptd.nsf/webmain/4B7775373E4AE64986256B6000691505?opendocument
Hope this helps! Let me know if you have further questions regarding this.
Best regards,
Yusuf Cavdarli
Applications Engineer
National Instruments