So if you try to save on a different slot, it won't work?
I had a bit of weird issue earlier on when saving. What I usually do is I will have two save files. One I save outdoors (slot 1), the other inside a dungeon (slot 2).
Well I had saved in town (New Sorpigal) and then saved inside Goblinwatch a short while later. When I went back to New Sorpigal and tried to save, it would save, but the new save didn't take. It still registered the 'old' save in New Sorpigal, before I went to Goblinwatch.
I eventually had to go into my save file, delete slot one save. And when saving now on slot 1, it works fine and overwrites the previous save.