I don't know if I understood your scenario.
But here are some suggestions:
- after using the navigate method, you can add a new line to wait for the new popup window, or a child element, or a property from the newly loaded page
- maybe the page is hidden in the background but the automation-driver (the one that sees the Tree elements) can see the elements and 'bypass' your assertion'. In this case, try to find an element from your page after is loaded and use WaitProperty method on it, for VisibleOnScreen property.
- try another way to assert your step (not based on navigate result method)