This happened to me as well, but also there were cells marked incorrect
(red font) when they were actually correct (no other cell in
row/column/square had the same number. I double-checked). After getting
stuck on a first pass, I tried to have the program "Fill all squares",
but it did not do anything. I cleared the numbers and notes I had on the
board and started over. As I was filling out the board, some numbers
would highlight red, but not be paired with anything. After finishing
the board, it did not acknowledge the win.

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Sudoku not acknowledging winning solution
https://bugs.launchpad.net/bugs/376996
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