Correct option is D
Given:
• Seven boxes (M, N, O, P, Q, R, and S) are kept one over the other.
• Only three boxes are kept below N.
• Only two boxes are kept between N and P.
• Only Q is kept above O.
• S is kept at some place below R and at some place above M.
From the given information, the arrangement will be.
1. Number the positions 1 to 7 from bottom to top (7 being the top-most position and 1 being the bottom-most position).
2. Since only three boxes are kept below N, N must be at the 4th position.
3. Only two boxes are kept between N (4th position) and P. This means P can be at either the 7th position or the 1st position.
4. "Only Q is kept above O" means O is at the 6th position and Q is at the 7th position (the top-most position). This eliminates the possibility of P being at the 7th position. Hence, P must be at the 1st position (the bottom-most position).
5. Now, the remaining vacant positions are 5th, 3rd, and 2nd.
6. Since S is kept below R and above M ($R > S > M$), R must be at the 5th position, S at the 3rd position, and M at the 2nd position.
The final vertical arrangement from top to bottom is:

Therefore, box M is at the second position from the bottom.
Final Answer Statement:
M is kept at the second position from the bottom.
Conclusion:
Thus, the correct option is (D).