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

-- 
Corrupt hints in Gnome Sudoku 2.24.1.1
https://bugs.launchpad.net/bugs/309968
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