NGUI should prevent you from messing up your atlas texture, but certain platforms / settings restrict max texture size. For example targeting ARMv6 / GLES 1.1 devices will cap the imported texture size at 1024. The actual atlas may be larger, like 2048, but Unity will import the texture capped as 1024, thus messing up everything you see. Forcing the texture import to be of larger dimensions fixed everything.