Overriding views default templates
Are the templates that are overriding your templates included in a Theme? Themes always take precedence over modules, so any template in a theme will always override the corresponding template from a module. You may want to consider re-phrasing your question to reference the original issue you are solving with your template files.

If you are referring specifically to Views output with your desire to create semantic markup, I would suggest the Semantic Views module.