I still do not understand the problem, at least based on the screenshot, which does not demonstrate any issue.
Perhaps the most important thing here is to understand that the repository explorer does not represent the model hierarchy (and thus has no effect on runtime behavior), but rather is a container for all models organized into packages. Packages (such as Content, List, Item, Header, ... in your screenshot) are created when certain templates, having the createSubPackage property, are used, as well as by the modeler himself (via right-click > New > Package). And models can be moved around from one package to another, without affecting the model hierarchy.
Does that help in clearing up anything? If not, please provide more information.
For best results, use the Firefox browser..