I've spent some time trying with a clean chroot, and I am unable to reproduce in a clean chroot, even when I copied all my apache config into the chroot. I tried to get all of the apache modules I'm using installed and activated in the chroot as well; but maybe I missed something.
I also tried copying all of /etc/ into my clean chroot, and was still unable to replicate the problem; although it still happens in the main root.