o_O I've got Blue Sphere just fine with S3D. In my experience if it fails to find what to do with a Locked-On cart, it just defaults to S&K (my EWJ used to do this, for some reason).
It seems to be something related to pin-passing in my opinion. I have a friend who had a problem running Sonic 3D using the 32x while it worked perfectly without it. However, it used to work always before. Wearing-off, anyone?