Via Randy Drisgill’s blog, this sage advice (as if you needed it, right?) on themes, master pages how SharePoint works to confound modifications and why you shouldn’t make any changes outside of your dev environment:
Disabling Themes on Master Pages
Turns out, the key to having SharePoint NOT apply the theme automagically is to have a master page that is NOT customized (unghosted). If you apply your custom master page from a Feature instead of customizing it with SharePoint designer, SharePoint will no longer add the meta tag and thus will not load the theme.
Word.
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