First of all, the clear is not necessary at all. Secondly you don't need to increment i and j because the for loops do that automatically for you. Third, you're not indexing NSSST so you're just overwriting a scalar every iteration. Maybe you want:
for i = 1 : 12
for j = 1 : 12 : 324
NSSST(i, j) = SST(:,:,j) - SSST(:,:,i);
end
end
