Why didn't Gretchen know Donnie at the end ?

Because the end was actually the beginning, and she hadn't met Donnie yet (and since he's dead, she never will)

She never met him as time was reversed and the jet engine crash happened before she ever knew of Donnie’s existence.

But seeing Donnie’s family, especially his mother, certainly had to make her feel a sense of familiarity. Hence, she waves at Donnie’s mom and glances at her kinda oddly. She felt a “strange” connection.

Time was reversed. Therefore, Gretchen and Donnie never met. Or at least that's my interpretation. Everyone has their own theory.

Which Gretchen?