Comment 4 for bug 309968

Its not just me then I have had the same problem in fact I went so far as to duplicate a game in an online sudoku and confirmed the numbers used were valid and the puzzle solvable.

It's related to the undo routines you add a tracker and get stuck and when you tell it to clear the tracker it seems to get stuck with the impossible squares.
 Even telling it to ignore the impossible squares it still doesnt recognise the completed game with valid values in every square.

in the one case I recall there were two pairs opposite each other each in a unique region two in the top row two in the bottom
they should have had 89 in the top and 98 in the bottom indeed it didnt really matter which way round the two pairs should go either position would have been valid.

However as I went to retrieve a saved messed up game it was restored with two of the squares cleared rather than completed and entering the correct values completed the game.

maybe its the case where two nearly identical sudoku's are valid that this causes the problem. clearing a square , heck clearing the board would not get rids of the x in the bottom left hand corner of the effected squares.

so as a work around saving and restarting the game seems to clear the bug, presumably only completed squares are recorded on a saved game without the history.

this is with
GNOME Sudoku 2.24.1.1 on ubuntu intrepid