For what it's worth, I also have this problem with very slow saving of
options.el after I've customized something. The weird part is that it
isn't always slow.
Customize something, Press save->very slow save, and 100% CPU. Press
C-g. Press save again->fast save.
You might want to check the size of your customization file after typing
C-g. That same thing has happened to me, and it turned out that my
customization file shrunk by a significant percentage. YMMV.
Chris