Do you have the min size property set in the children node(s) of the VBoxContainer?
Last I knew, the VBoxContainer will size the items based on the value in the min size property. I believe this is to make it easier for the VBoxContainer to find a size that will fit all of the children nodes, where the largest min size property is used as the size for all of the child nodes within the VBoxContainer.
Regardless of what it is for, I believe setting the min size property will allow you to change the size of the children nodes.
Hopefully this helps!