Saving in the graveyard by the poor quarter was deliberately disabled to avoid a bug/glitch in that area.
The game will disable saving if it thinks you are in the middle of a cut scene. Did you maybe start the scene with the knight on the road to Verdistis, but not finish it? One person ran into this problem after seeing the disappearing gem south of the poor quarter's graveyard, but not following it to the meeting / cut scene. If you can save just before entering, but not after, the game may have a problem with the snoozing guard, who is suppose to talk to you as soon as you step towards him.
