Help Understanding Aegir
(2nd Attempt!)
It almost looks like the symbolic link they have you create in step 3.1.1, is not working correctly and may be causing this issue.

I don't know anything about the differences between Debian and RH 5.5, but maybe RE doesn't have a /etc/apache2/conf.d directory, in which case you would have to manually add an include line into httpd.conf

Cheers.