Ok, this is still perplexing me, as I have a new version from git and I still get the error. The following is complete list (sorry for the long email!) of what I have done:

* Get a fresh copy of =org-mode= from git and byte-compile:

#+begin_src: sh
cd ~/install/org-mode
mkdir new_git_clone
cd new_git_clone
git clone git://orgmode.org/org-mode.git
cd org-mode; make &> make.out
ln -s ~/install/org-mode/new_git_clone/org-mode ~/install/org-mode/current
#+end_src

During the =make= process, I noticed quite a few warnings. An example is below (for a complete copy of =make.out=, see http://astro.sunysb.edu/cmalone/nolink/make.out

========================================================================
org.el:19993:1:Warning: the function `parse-time-string' might not be defined
    at runtime.
org.el:19993:1:Warning: the following functions are not known to be defined:
    table--at-cell-p, org-clock-update-mode-line, org-default-export-plist,
    org-infile-export-plist, org-inlinetask-at-task-p,
    org-inlinetask-toggle-visibility,
    org-clock-save-markers-for-cut-and-paste,
    org-agenda-save-markers-for-cut-and-paste, org-id-get-create,
    dired-get-filename, org-id-store-link, iswitchb-read-buffer,
    org-agenda-copy-local-variable, org-attach-reveal,
    org-inlinetask-remove-END-maybe, org-agenda-skip, org-format-agenda-item,
    org-agenda-new-marker, org-agenda-change-all-lines,
    org-columns-number-to-string, org-columns-get-format-and-top-level,
    org-columns-compute, calendar-absolute-from-iso,
    calendar-iso-from-absolute, org-id-locations-save, org-id-locations-load,
    cdlatex-tab, org-export-latex-fix-inputenc, orgtbl-send-table,
    org-inlinetask-in-task-p, org-inlinetask-goto-beginning,
    org-inlinetask-goto-end, org-inlinetask-outline-regexp,
    fill-forward-paragraph, beginning-of-visual-line,
    org-agenda-set-restriction-lock, speedbar-line-directory,
    org-agenda-maybe-redo
Wrote /home/cmalone/install/org-mode/new_git_clone/org-mode/lisp/org.elc
========================================================================

Are such warnings normal?

* Make sure my =.emacs= file is pointing to the correct location
Here is a copy of the =org-mode=-relevant sections of my =.emacs= file:

========================================================================
;;
;; org-mode stuff
;;
(add-to-list 'load-path "/home/cmalone/install/org-mode/current/lisp")
(require 'org-install)
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)
(setq org-log-done t)

;; using the prop_just class
(require 'org-latex)
(add-to-list 'org-export-latex-classes
             '("prop_just"
               "\\documentclass{prop_just}
               [NO-DEFAULT-PACKAGES]
               [PACKAGES]
               [EXTRA]"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
(add-to-list 'org-export-latex-classes
             '("letter"
               "\\documentclass{letter}
               [DEFAULT-PACKAGES]
               [PACKAGES]
               [EXTRA]"))

; org-babel stuff
(org-babel-do-load-languages
'org-babel-load-languages
'((org . t)
   (emacs-lisp . t)
   (python . t)
   (latex . t)
   (perl . t)
   (sh . t)
   (C . t)
   (ditaa . t)))
(setq org-confirm-babel-evaluate nil)

;;
;; for YASnippet
;;
(add-to-list 'load-path "~/.emacs.d/plugins/yasnippet-0.6.1c")
(require 'yasnippet)
(yas/initialize)
(yas/load-directory "~/.emacs.d/plugins/yasnippet-0.6.1c/snippets")

;; define backtab (essentially Shift-Tab) for org-mode
(global-set-key (kbd "<backtab>") 'org-shifttab)

;; Make TAB the yas trigger key in the org-mode-hook and enable flyspell mode a\
nd autofill
(add-hook 'org-mode-hook
          (lambda ()
            ;; yasnippet
            (make-variable-buffer-local 'yas/trigger-key)
            (org-set-local 'yas/trigger-key [tab])
            (define-key yas/keymap [tab] 'yas/next-field-group)
            ;; flyspell mode for spell checking everywhere
            (flyspell-mode 1)
            ;; auto-fill mode on
            (auto-fill-mode 1)))
========================================================================

* Attempt an export of the =org-mode= file found here: http://astro.sunysb.edu/cmalone/nolink/python_class_lstings.org

Exporting this to PDF, HTML, or ASCII (I didn't try other forms) results in the following error in the *Messages* buffer: 'Invalid read syntax: "#"'. I turned on =debu-on-error= and the *Messages* and *Backtrace* buffers can be found here:
http://astro.sunysb.edu/cmalone/nolink/messages.txt
http://astro.sunysb.edu/cmalone/nolink/backtrace.txt

PS: I had already written most of this before I just saw your email - hopefully this helps...

Chris

On Tue, Feb 22, 2011 at 10:06 AM, Chris Malone <chris.m.malone@gmail.com> wrote:

Hi Eric,

I removed all the compiled elisp files, and the problem still persists. Next step will be a completely fresh install from git; my current version is up to date, but maybe there was some conflict that git didn't complain about...

Chris

On Mon, Feb 21, 2011 at 2:48 PM, Eric Schulte <schulte.eric@gmail.com> wrote:

Chris Malone <chris.m.malone@gmail.com> writes:

[...]

>
> I added =(setq org-confirm-babel-evaluate nil)= to my =.emacs= file, and indeed I am not asked about evaluating the code block, but I'm still getting the invalid
> syntax error when =org-babel-exp= is called the second time on the =emacs-lisp= code block.? I should mention that this is somewhere in the byte-code, as the error
> is:
>
> byte-code: Invalid read syntax: "#"
>
> in the *Messages* buffer.? I still don't fully understand why it should be evaluating that code block twice.
>

Hmm, it may be worth cleaning out all compiled .elc files from within
Org-mode, the calling org-reload, and see if the problem persists.

Best -- Eric

>
> Chris