I received an email last February from a Spanish undergraduate, Nil Mamano, with a proof that this problem is indeed NP-complete, by reduction from Hamiltonian path in grid graphs. I don't know that it has been published anywhere yet. The reduction replaces each vertex of the grid graph by a 2x2 block of 1's, and each edge, face, or missing vertex by a 2x2 block of 0's. The input sequence alternates between subsequences of four 1's and four 0's for as many times as is needed to cover all the vertices, then fills out the rest of the sequence with 0's. To match the input sequence, a path through the grid must align the subsequences of four 1's with the 2x2 blocks of 1's from the reduction, forming a Hamiltonian path; if such a path exists, it's always possible to do this in a way that allows the rest of the matrix to be covered by the remaining zeros at the end of the sequence.