Let X be your N-by-2 matrix. Then the following code will separate X into a cell array Y, each element of which is a slice of X according to the second column value:
idx = 1+[0; find(diff(X(:,2))); size(X,1)];
n = numel(idx)-1;
Y = cell(n,1);
for i = 1:n
Y{i} = X(idx(i):idx(i+1)-1,:);
end
