The desired minimum is 33⋅34=1122. More generally, for n=3k+1 instead of 100 the answer is Smin=2(1+⋯+k)=k(k+1). For clarity we state separately a fact used later in a proof of the lower bound S(α)≥2(1+⋯+k) for each permutation α of 1,2,...,3k+1.
Claim. If 2k distinct natural numbers are divided into k pairs uj,vj with uj<vj, j=1,…,k, then v1+⋯+vk≥2(1+⋯+k).
The justification is by induction on k, with obvious base case k=1.
For the inductive step k−1→k choose the labeling so that vk:=maxj=1kvj. Ignore uk and vk for the time being, and apply the inductive hypothesis to the remaining 2k−2 numbers. This gives v1+⋯+vk−1≥2(1+⋯+(k−1)). So it is enough to prove vk≥2k in order to complete the inductive step. We have vk>vj for all j=1,…,k−1 by vk=maxj=1kvj. In addition observe that vk>uj for all j=1,…,k. This holds for j=k by hypothesis. Suppose that vk<uj for some j=1,…,k−1. Then uj<vj implies vk<vj, which contradicts the maximum choice of vk. In summary there are 2k−1 distinct natural numbers smaller than vk, namely u1,…,uk,v1,…,vk−1. Hence vk≥2k, completing the induction.
Now let α=(a1,a2,...,a3k+1) be any permutation of 1,2,...,3k+1. Divide a1,a2,...,a3k into k triples Tj={a3j−2,a3j−1,a3j},j=1,…,k. Let uj and vj be respectively the smaller number and the middle number in Tj. The 2k numbers uj,vj,j=1,…,k, are distinct. Then the claim above gives v1+⋯+vk≥2(1+⋯+k). Since v1,…,vk are marked numbers (in general there are more of them), the sum S(α) of all marked number in α also satisfies S(α)≥2(1+⋯+k).
The equality S(α)=2(1+⋯+k) is attained for the following permutation of 1,2,...,3k+1: 3k+1,1,2,2k+1,4,3,2k+2,6,5,2k+3,...,2k−2,2k−3,3k−1,2k,2k−1,3k.
The marked numbers are precisely 2,4,...,2k, hence S(α)=2(1+⋯+k). This completes the proof of Smin=2(1+⋯+k)=k(k+1).