If you are adopting a minimal-is-best approach to templating your Magento Enterprise store (ie.
local.xml method), you'll soon run into some odd behaviour with the theme fallback. Typically, a Magento store will try to load a file in the following order
./app/design/frontend/custom_package/custom_theme ./app/design/frontend/custom_package/default ./app/design/frontend/base/default
However, if you are using Magento Enterprise and which to use the default Enterprise theme as a basis to serve your new theme, you need to alter the fallback method to support checking the Enterprise theme too. It should really be like this by default, as otherwise it would involve copying and pasting of many files simply to achieve the same output. So rather on Enterprise, it would be preferred to do the following,
./app/design/frontend/custom_package/custom_theme ./app/design/frontend/custom_package/default ./app/design/frontend/enterprise/default ./app/design/frontend/base/default