(click image for larger view)

Well, some other things I can think of:

The target figure should be selected before the conformer is loaded.

If you save the conformer back to the Figures palette on its own (not as part of a compound figure group with the target figure), that will break the super-conforming.

In the above image, the slaving code on your left hand side does not super-conform, the slaving code right does. The difference is the absence of the colon and number (:#) in the right hand slaving code.