Thanks alot for all the tips. I definitely think that some of the items were grouped, and I've had a ton of issues with "junk" data in the outliner from shape nodes in the past. All these are good ways to fix the problem. Something that also seems to reset the associations are combining different items together. But that…
There are weird things that can happen in Maya. It might be a case of the Shape node being added to the layer but the transform is not. I can't replicate this issue now but try this script below and see if it helps. Add it to a shelf button, select the problematic objects and click it. // Get selectionstring $selection[] =…