Output of a discrete transfer function goes unbounded when numerator and denominator are given as external input?

I compared the results of a discrete transfer function block in two cases: 1.numerator and denominator given internally 2. numerator and denominator given externally as vectors (matrices produced using a matlab function). The output in the later case goes unbounded after a particular point while in the case of former the output remains bounded.The only change that I noticed was that the "optimising by skipping dividing by leading coefficient (a0)" checkbox is unchecked in later case while it had to be checked in the former case.Why does this problem arise and how can it be solved?(I need to use the second case.)