I tried to replicate this issue locally, but the css class I set applied correctly over the page after I removed the Basic theme. Here are the steps I followed, so let me know if I missed something here
1. Created a class and template for it
2. Created a simple css that sets background of the body.
3. The class, template and css were embedded resources
4. In the template I added
<sitefinity:ResourceLinks ID="ResourceLinks1" runat="server" UseEmbeddedThemes="true">
<sitefinity:ResourceFile Name="Telerik.Sitefinity.Samples.Resources.Layout.css" Static="true" AssemblyInfo="Telerik.Sitefinity.Samples.Reference, Telerik.Sitefinity.Samples" />
5. Then I dropped the control on a page
6. I went to the backend >> Settings and removed the Basic theme
7. I returned back to the front end and request the page - the css class I used was properly applies.
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