Select your UI Root and hit ALT+SHIFT+P to make it pixel-perfect. Maybe it is, as you said, a coincidence, and something got moved in the hierarchy making it not pixel perfect. Also note that in NGUI 3.0.6 and earlier you need to have your widgets under a center-based UIAnchor with half-pixel offset checked, and UIRoot needs to be set to PixelPerfect as well.