hooooo I did something interesting that seems to fix my issue
if (rootFeature.GetTypeName2() == "Reference")
var selMgr = (ISelectionMgr)model.SelectionManager;
root = selMgr.GetSelectedObject6(1, -1) as Component2;
head = true;
I'm forcing a new selction and set it as my root component seems to do the trick.
Hope it will help someone.