I think people are angry at this problem and are in danger of shooting the messenger here...
I do have a question though... are you saying the problem is fixed for you with the 10.11.1 update? or did you have to go through the steps you suggested earlier. ?
I tried with a guest user as a quick check as you suggested earlier but I still had no incoming mail sound...
One odd thing I noticed when I logged in as guest was that the mountain range screen image was sharp. On my normal log in this is very out of focus.. I assumed it was Apple being arty but perhaps there is another problem as well - which might suggest there are corrupted system files I suppose.
I am currently downloading the installer again, do you know where it is downloaded to by any chance? I have downloaded it before but it does not appear on my machine...
thanks