Multistore with 2 Domains – Theme Issues in Magento

Using this knowledge base entry from Magento I have tried to set up multiple domains to access my Magento store

System > Manage Stores

in the menu System > Manage Stores I have the following

System > Configuration

in the menu tab of System > Configuration I have set the Base URL with trailing slash (/) for both Unsecure and Secure

in the design tab of System > Configuration (both themes I am trying to use are in default)

Current Package:     [ default     ]

Translations:        [             ] (blank)
Templates:           [             ] (blank)
Skin (Images / CSS): [             ] (blank)
Layout:              [             ] (blank)
Default:             [             ] (blank)

Originally I had tried using this method to set the theme, it had not worked, then I found the tutorial and went to that method.

.htaccess

in my .htaccess I have (which should cover www.site1(2).com and also site1(2).devenv.com)

SetEnvIf Host .*site1.* MAGE_RUN_CODE=base
SetEnvIf Host .*site1.* MAGE_RUN_TYPE=website

SetEnvIf Host .*site2.* MAGE_RUN_CODE=c_base
SetEnvIf Host .*site2.* MAGE_RUN_TYPE=website

In index.php I echoed out the env variable to make sure I was getting what was needed, and did get base on site1 and c_base on site2

System > Design

I am setting my template using the System > Design menu item and only 1 theme works for both sites (default/mycustomtheme)… none of the default themes work (default/default, default/modern, rwd/default)

Results

If I attempt to load any theme other than this custom theme I get a page with no CSS files loaded, no theme files loaded (though if you search for a file that falls within the theme it is there, for instance http://site1.devenv.com/skin/frontend/default/mycustomtheme/images/footer-logo.png, the file is there and exists, along with the css files (there is no script or link for any theme files in the header, in fact there is nothing between the opening head and closing head tags)

/skin/frontend/default/mycustomtheme/ works for all stores
/skin/frontend/default/{default|blank|iphone|modern}/ does not work for any store
/skin/frontend/rwd/default/ does not work for any store

I do know that the site1 and site2 are both being fetched properly as they have different home page cms, and the proper home page cms is being called with the proper url

Questions

How can I get the ability to alter themes within my stores (what am I doing wrong or missing)?
Could it be a server setting blocking this? Is there something server side I should be looking at?

log

in my system.log file I have the following error when trying to load a new template

2015-03-05T15:20:50+00:00 CRIT (2): Not valid template file:frontend/base/default/template/ec/header.phtml
2015-03-05T15:20:51+00:00 CRIT (2): Not valid template file:frontend/base/default/template/ec/footer.phtml