I played the web version but I don't think I ever opened two copies of the game. But my mouse has been double-clicking a lot lately, so maybe when I opened the game for the first time?
I think I initially was in the mess hall or the galley, then moved down to the explosives room to re-check the testimony of the officer there. There I noticed that the entries completely disappeared (the order of events and the end conclusion), but after I moved back up they were there again, but with the order of events for 'last night' in the wrong order.
Btw, I did really enjoy the game!