That's because the output of your Matlab Function block is the result of your for loop. The output is not the result of each iteration. You can use persistent declaration without a for loop, because Simulink will run your function automatically each step.
function x=fcn(k)
persistent i
if isempty(i)
i=0
end
i=i+1
x=i
if i>5
x=k
else
x=i
end
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