I am a native US English speaker and this answer is from my own experience. It is not a academic answer. Both sentences are correct, but the wording of the second sentence is a bit off. I would rephrase it to say "My mother asks my sister what's the matter with her." With "what's" being a contraction of "what is". Also, I'm not sure if you're using the intended verb tense for "asks". If she did it in the past, even a few seconds ago, I would use "asked". If she is continually bugging her about it then I would use "asks" as you are.