For the task, at hand, filing Berkheimer, it doesn't matter why box 16 doesn't match box 1. Just use the box 16 amount as they said.
But as @JosephS1 said, it is not unusual for them not to match. The difference could be any pretax benefit(s) (e.g. health insurance). Your employer may be the only place to get a definitive answer.
In Ohio, the city (local) tax agencies want you to use box 5 (medicare wages), if box 18 is empty.
