Permutations with forbidden subsequences
It's NP-complete for $k=3$ by a reduction from betweenness. In the betweenness problem, one is given $n$ items to be totally ordered, and constraints on some triples of items forcing one item of the triple to be between the other two. In your problem, the same constraint can be forced by forbidding all the subsequences on three elements that do not place the middle element in the middle. But betweenness is known to be NP-complete: see J. Opatrny, Total ordering problem, SIAM J. Comput., 8 (1979), pp. 111–114.