Plan is a non calendar plan ending 9/30. For purposes of payroll cutoff dates, do you use the pay period ending or the date check issued? Example: Pay period endins 9/27 but check is issued on 10/4. Is this period included in the just ended plan year end or is it the first pay period for the new plan year end?

Look at the plan's definition(s) of compensation. It should tell you. Our documents say to use compensation actually paid during the period.

Especially look at the plan's 415 amendment. Before that time, the 'first few weeks' rule was operational. Not anymore with the 415 amendment, so Kevin's right, it should be spelled out now in your plan language.