Addition to the above information. When looking at my last save from my last game when I save near the end battle I found an extra file in the SAVEGAME.sav called pc.utc that contained the information about my character. Do not know why it did not show up in the other save files but I'm checking it out.
This probably happens when:
the PC is switched out of the active party during the Leviathan mission.
I noticed this as well, when I was looking into editing the savegames, and it seems to show up around that time.