Did you try a different install DVD not CD? I ask as I recall a fedora bug from awhile ago (fc21 2014/15ish) with petitboot where it would not recognize specifically a DVD install media to show up in the boot list. It had to be done manually as you have done. It has to do with how it reads grub. It did not have support ['FOR' loops] in grub.conf/grub2.conf
This at least would confirm if the issue is specific to Qubes installer which is just a slightly modified anaconda installer i.e. fedora SOP (less likely) or an issue with petitboot handling of DVD mentioned above.
Here is what is needed to be added to petitboot code and speaks to the issue:
http://git.ozlabs.org/?p=petitboot;a=commit;h=1b272c7d47390077eee0a0638329b1a7df521329
What version of petitboot do you have? It should print something like this: dev.20141013 or maybe 32e2eac7 ? You could look to confirm you are using a version that had these changes applied. Confirm those additions were actually add as well. I only looked quickly so did not confirm.
I know you maybe set on DVD for a some reason i.e. extra security; but honestly USB has for years been the most trouble-free way to install Qubes.
Sorry I can not be more help but you could check the grub.conf from a USB install stick after you confirm it works for your setup and does not fail at same point