Duane,
Not to resurrect an old thread, but I just wanted to confirm that I am have encountered this same issue as well. Up until now, I have been publishing our local gov basemaps from a file gdb. We have since moved it to an enterprise database to help make the updating process a little easier. Since trying to publish the basemaps from the sde database, I have come across the same errors with the geometry queries on the SHAPE.STArea and SHAPE.STLength fields. I do find it odd that ESRI included these queries in their basemaps, and never came across the bug before release. Surely they must have tested in an enterprise environment?
Did you ever find a satisfactory workaround?
Thanks,
Andrew