I've got (set-face-attribute 'default nil :height 100) in my init.el because I find the default font size a little too large. However, it doesn't get executed when emacs is loaded.
I don't have an init.elc file that's not representative updated version of my init.el, and I know the rest of the my init.el is being executed.
There are no other (set-face-attribute ...) sexps after it that could be overwriting it.
Going back in to my init.el after loading emacs and executing it myself sets the property correctly (i.e. for all buffers (but not new frames), persistently)