Reproduction steps:
1. Create a new project and ensure that the Game window is visible
2. GameObject > UI Toolkit > Panel Renderer
3. Select newly created GameObject and press “New” button to create and attach UXML Template
4. Double-click newly created UXML Template to open UI Builder window
5. Drag and drop any two Elements and a Scroll View into the Hierarchy (e.g. Visual Element and List View)
6. Change background colors of the two Elements (Inspector > Inlined Styles > Background)
7. Save changes and click on Game window to focus it
8. Open the UI Builder window again

Actual result: Element background colors switch places in the Game window
Expected result: Game window remains unchanged

Reproducible with: 6000.3.0a5 (36d7e9fd6645), 6000.4.0a1, 6000.4.7f1, 6000.5.0b8, 6000.6.0a5
Not reproducible with: 6000.0.75f1, 6000.3.15f1, 6000.3.0a4

Reproduced on: Windows 11, macOS Tahoe 26.4 (M4)