Just for reference, in case anyone else runs into this problem (and doesn't think to search the Virtualmin.com forums where it's been discussed a few times), this happens if apache2 has been preinstalled on the system before the install script. I don't know why it doesn't get replaced by apt-get, and I've never been able to figure out how to make it apt-get actually do the right thing, but it is easy to fix.
apt-get install apache2
At the end of the installation process. "apt-get update" might also do the trick. It should install the version from our repositories (labeled with a "vm" in the version number).
I haven't spent much time trying to work around this, as the way we deal with Apache and suexec on Debian systems has since changed, and doesn't require our custom build anymore. When the next LTS release of Ubuntu is released, it will use this new method. Or, you could get it today by just using Debian 5; Ubuntu doesn't really have any benefits over Debian on the server (and it has a couple of annoying quirks that Debian does not).
Anyway, CentOS 5 is also a great distro for hosting. I'm not suggesting it was a mistake to switch...it is, by far, the most popular distro for virtual hosting (has about 75% of the market, as far as I can tell, based on our user numbers).