The mailing list thread on this discussion has died-out, so I am reviving the issue here.
Webmin uses 'apt-get -y install' to upgrade packages. This approach causes problems relating to package dependencies.
For example, whenever I upgrade the apache2 package, libapache2-mod-php5 is removed in the process and never reinstalled. This causes Apache to fail to start after the upgrade (due to syntax errors resulting from libapache2-mod-php5's absence). I have to reinstall libapache2-mod-php5 manually every time.
Initially, I thought that this was a problem with Ubuntu's apache2 package, and I opened a ticket ( https://bugs.launchpad.net/ubuntu/+source/apache2/+bug/969426 ), but the folks at Ubuntu clarified the issue and explained why 'apt-get -y install' is not the right approach to upgrading packages.