Keep in mind that I still have the same start scene it's just that the ui only shows up if the current scene in the editor is the ui scene.
My ui isn't visible if I start my game from another scene.
MrSniff it sounds like your new scene is instantiating on top of whatever was there.
nodes are drawn in the order they appear in the tree, the first nodes are rendered at the back, the last nodes at the front.
and since your UI was in the start scene, it is probably being buried under.
create a node2D and instantiate your levels there, so that it looks like this:
background
level
foreground
UI