Hi Zachary,
I've got exactly the same issue on AGS 10.3.1, exactly the same and I'm knocking my head against the wall.
No warning with data store properly registered and ArcGIS Server that keeps uploading the gdb in the v101 folder with no warning about data that will be uploaded.
Were you able to fix that issue ?
Thanks
Ok, I've found a solution for the next ones facing that issue : you need to publish your service from ArcMap (don't ask me why)
Alex.