Hi Bob,
I think I've narrowed down the problem you might be having. Does it sound something like this?:
You're editing a population. Say you have an instance whose bounding box crosses over the selection handle for another node. When you mouse over the object the instance bounding box will highlight but when you move across the other selection handle the bounding box highlight will remove. As you move further, away from the other node's selection handle, the highlight will come back. All this is while the mouse is within the instance bounding box.
Is that similar to your problem?
Regards,
Jo