Do you need one of the abilities the css customization gives you, beyond what you can do directly? For changing the colors, you can do that directly with the palette of the widget, which should preserve your style.
Also, remember that style changes are inherited, so if any widget containing the tree on the right has a different style than any one containing the tree on the left, that may cause the changes as well.
Beyond that, I would think that this appears to be a Qt bug, if indeed the only difference is the css style sheet.