I'm not sure I understand. IRIX 6.5 is an entirely different version of IRIX than 5.3, so naturally there are small changes to the UX, like different backgrounds and different color schemes. And likewise, if what you installed on the emulated Indy was IRIX 5.3 (as it would have to be since it's all that worked until yesterday), it's not going to magically become IRIX 6.5 unless you create a new CHD and install IRIX 6.5 onto it.
