<p>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 --debug-init". I've found some references to font-related resizing but this behavior doesn't seem to be limited to that (e.g reappearing menus and toolbars). </p>

<p>Does anyone have any additional information about the emacs initialization process?
Does it load /etc/emacs/site-start.d  files before or after the .emacs, and are there any other locations it loads by default?</p>

The sequence of the Emacs initialization is the following (at least, for Emacs 22):
Load the file
debian-startup
(.el or .elc) found in
load-path
(usually,
/usr/share/emacs/site-lisp/debian-startup.el
or
/usr/share/emacs22/site-lisp/debian-startup.elc
) and call the function
debian-startup
defined in this file.  This function loads all files in
/etc/emacs/site-start.d/
and
/etc/emacs22/site-start.d/
.
Load
site-start
(.el or .elc) found in
load-path
.
Load your init file
.emacs
,
.emacs.el
or
~/.emacs.d/init.el
.
Load a default init file
default.el
or
default.elc
.
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.