One register_sidebar function works, the other doesn’t?

If I had to venture a guess, the problem is that your first register_sidebar() gets called in functions.php, and hooked into widgets_init, but the second one gets called in the head, and therefore NOT hooked into widgets_init. I don’t know the impact of registering a sidebar other than at widgets_init.

Is there any particular reason that both calls can’t be called in functions.php and hooked into widgets_init?