After installing 4.0 Beta 2, I created a new project and copied over all files from my custom theme that was working in Beta 1.
I created the theme under Settings/Appearance/Frontend themes, and created 'My Theme', with the following value for Path: ~\App_Data\Sitefinity\WebsiteTemplates\MyTemplate\App_Themes\MyTheme
Applying the theme didn't work, so I fired up Firebug to see if the css was being sent down to the browser. Apparently there is some permissions issue:
<link rel="stylesheet" type="text/css" href="/MyApp/App_Data/Sitefinity/WebsiteTemplates/MyTemplate/App_Themes/MyTheme/global/style.css">
21 <h2> <i>HTTP Error 403 - Forbidden.</i> </h2></span>
23 <hr width=100% size=1 color=silver>
25 <b>Version Information:</b> Telerik Web Server 4.0.676.0
Has something changed with security/permissions in Beta 2 that I need to address?