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I have an AWS EC2 instance running Ubuntu 10.10. I just migrated over my WordPress Multisite install and have that working.

With that I have a *.domain.com as an alternate server name on my Virtual Server for domain.com so that it works for any additional blog I add beyond the ones I have now. The problem is that I have two subdomains that I don't want WordPress to handle. One works media.domain.com the other doesn't sub.domain.com.

Any ideas on what I can do to get this to work?

All of this has been setup using Webmin.

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Apache config really depends on the loading order, it analyzes and configured the Virtual Hosts, you just need to make certain that the definition for those subdomains is always loaded before the catchall (*.domain.com) config

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Which config file might they be defined in on Ubuntu? – Mike Wills Jan 25 '11 at 14:59
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They should be defined as files in /etc/apache2/sites-available. These are sym-linked to /etc/apache2/sites-enabled usually with an ordering prefix like 000, 100, 200, etc. – BillThor Jan 25 '11 at 15:10
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