Hello,
Due to various initial conditions rarely the autotune algorithm may fail to calculate the PID loop parameters properly. In that case the best thing to do is to manually tune the motor. Please see the following link for more detailed information on this:
http://zone.ni.com/devzone/conceptd.nsf/webmain/4B7775373E4AE64986256B6000691505?opendocument
Hope this helps.
Best regards,
Yusuf C.
Applications Engineering
National Instruments