I've discovered another, somewhat similar phenomenom. Adjustments to the Z axis aren't shown, unless I precomp. This happens even if all the layers are 3D.
File it under the "one more of those CS6 bugs" category. Though you might try to check, whether the issue actualyl occurs when only running with the internal display. You could simply be running out of resources for all that hardware acceleration crap they threw into the program.
Are you using one of the orthographic camera views like "Front"? These views eliminate perspective, so can have some unexpected results.
This fixed it!
When I checked, all the cameras were set to "front". This seems to be what AE defaults to now, instead of the active camera when you turn 3D on.
Thank you for ending a frustrating hour...!