I don't have much time to play, so I pick up the game and play the story a few minutes at a time. Every time I leave the game I have to retrace 3 or 4 checkpoints (real waypoints and mainquest advances). It happened all throughout the game. During ACT I I had to talk to Eldric several times in the burned campment and interogate the dying soldier, it didn't save my progress until after I started the Prince's quest under the sewers. It happened many many times. I don't know if that's intended.