As a workaround, you can move the Feature Classes out of the Feature Dataset, upgrade the precision of Feature Classes and Feature Dataset using the 'Upgrade Spatial Reference' tool. Then move Feature Classes back inside the Feature Dataset.
Or you can simply copy your data into a File Geodatabase (this will convert them into High Precision) and back into the sde geodatabase.
But, as Craig mentioned, you should contact ESRI Technical Support so that they can troubleshoot this issue properly.
Regards,