A couple things to check for:
Are your *.d.ts files part of your project (via include or files)? If not, TypeScript won't check those as part of your project, obviously.
Do you have skipLibCheck: true in tsconfig.json? This will prevent TypeScript from checking *.d.ts files
Do you expect TypeScript to always check your whole project? This won't happen for performance reasons. With Atom-Typescript, you can force a complete typecheck of the project by running typescript:check-all-files command (bound to F7 by default) -- it might take a while depending on the size of your project and whether you're using any language service plugins.