It appears that this was caused by a patch to the Allegro elisp files made by one of our developers. I attached to the Allegro lisp process with gdb and saw that it was also hung on __select_nocancel(). The patch to elisp removed an initialization message from emacs to the alisp subprocess. My best guess right now is that this meant Allegro caught a message meant for emacs through an inherited file descriptor. Is this possible?
Thanks, Andrew Myers