The way to avoid the glitch is to not change your lightsaber crystals or costumes. The same thing happened to me when I beat the game on Sith Warrior and I was pissed. I just replayed the game on the Sith Master setting with a new save file and I didn't touch anything it worked for me. I was worried though because on the last level there was no side objective and I thought it had glitched on me but there just isn't one for that level. I'm talking about the 360 version.