I might be visiting the doctor as well. Jason is still working on the new Repair utility, but I have been seeing reports of folks seeing the new doctor and all of the music and photos have remained. I've been tweaking, untweaking and such and like you certain patches won't take anymore.
In the future though you are supposed to take off the theme before running the EPR. I did it by mistake and it left all the theme icons and such. What I did to get it back was install another theme via QI, the took it off, then re insatlled the same theme that was stuck and it worked.