The Optimized Image should be applied as the last step, on top of other changes you've made to an image first. Check out the Quality Control (
link1) guide, as well as the Preset (
link2) guide to get a feel for this kind of information. The layers and ordering matters a lot in Windows, especially with NTLite. The basic order goes like this: integrate windows updates and process, remove components and process, add registry tweaks and process. I also went and updated the first post on this Optimized Image thread today to make a note about this.