Egads...This is all wrong. ("Gromit! These are the wrong trousers, Gromit...and they're all wrong!")
Obviously our upgrade from GPL to Professional process has been drinking the Fail-Aid.
I'm guessing that you installed initially using the wbm modules, rather than using the install script for Virtualmin GPL? I think that's the way to end up with the upgrade not enabling the Virtualmin Professional apt repository and such.
So, you probably want to get the apt repo setup. The virtualmin repo line looks like:
deb
http://SERIAL:KEY@software.virtualmin.com/debian/ virtualmin-etch main
Where SERIAL and KEY must be replaced with your serial number and license key (found on
http://www.virtualmin.com/serial/ )
Then you can try upgrading Apache again. (You may also want to move your install over to a deb-based one, and use the Virtualmin Package updates module to help you stay on top of updates. Once apt is configured, you can get it via "apt-get install webmin-security-updates".)