Odd behavior loading emacs on ubuntu, there seems to be some initialization that goes on that is not in the .emacs nor in any of the files emacs reports loading through \"emacs
The sequence of the Emacs initialization is the following (at least, for Emacs 22):
I also suggest you reading the section "Emacs startup strategy" in /usr/share/doc/emacsen-common/debian-emacs-policy.gz for more Ubuntu/Debian specific information. To find the reason of odd behavior you can start emacs with the argument --no-site-file and load these init files one by one until you find a file that causes this behavior.
I've found this official document that introduces the emacs init steps: http://www.gnu.org/software/emacs/manual/html_node/emacs/Init-File.html
When Emacs is started, it normally tries to load a Lisp program from an initialization file, or init file for short. This file, if it exists, specifies how to initialize Emacs for you. Emacs looks for your init file using the filenames ~/.emacs, ~/.emacs.el, or ~/.emacs.d/init.el; you can choose to use any one of these three names (see Find Init). Here, ~/ stands for your home directory.