I'm not sure if I'm understanding you correctly... but in order to complete that part of the unseeing eye quest you need to go inside the temple behind the diseased ones and combat the demon there by pelting it with healing spells.... Though you must have already done this if you obtained the rod...
Anyways, once you have done that talk to the avatar that appears and, then again to the diseased ones. You should get a cut scene and you will all end up inside the temple, where you have to persuade the diseased ones to invoke their god....
Although admittedly, I have always completed everything down there at the same time.. I don't know how leaving and then returning, once the beholder is dead, affects things....
Regarding your technical problems, try downloading the most recent patches (from both Bioware and Balderdash); this solves most of the problems with ME and XP to the best of my knowledge. You may also want to check your game's config and frame rates.