Three-fold Repetition Confusion

I just played a USCF rated game where my opponent had less than 5 minutes left but he was still notating. Since he notated on an electronic device, it auto-registers a draw for him when it is three-fold repetition. It did, but my opponent didn't notice and played on. A few moves later, my opponent got checkmated. Only then did he notice that the device registered a draw. Does this count as a win for me or a draw? 

Thanks! 

His notation device should not give notification of triple repetition of position. However, it has to be claimed, it's not automatic, and since your opponent did not claim it the checkmate is all that counts.

3-fold repetition has to be claimed, 5-fold repetition is automatic. Even if 5-fold occured, the result stands once scoresheets are signed.
9.2.1
The game is drawn, upon a correct claim by a player having the move, when the same position for at least the third time (not necessarily by a repetition of moves):
9.2.1.1
is about to appear, if he first indicate his move by writing on the paper scoresheet or entering move on the electronic scoresheet, which cannot be changed, on his scoresheet and declares to the arbiter his intention to make this move, or
9.2.1.2
has just appeared, and the player claiming the draw has the move.
9.2.2
Positions are considered the same if and only if the same player has the move, pieces of the same kind and colour occupy the same squares and the possible moves of all the pieces of both players are the same. Thus positions are not the same if:
9.2.2.1
at the start of the sequence a pawn could have been captured en passant
9.2.2.2
a king had castling rights with a rook that has not been moved, but forfeited these after moving. The castling rights are lost only after the king or rook is moved.

9.6.1
the same position has appeared, as in 9.2.2 at least five times.

8.7
At the conclusion of the game both players shall indicate the result of the game by signing both scoresheets or approve the result on their electronic scoresheets. Even if incorrect, this result shall stand, unless the arbiter decides otherwise.

https://handbook.fide.com/chapter/E012018