I don't know for sure if updating the patch and deleting the files in the dynamics folder will fix the problem, but that would be the most likely solution and the easiest to try. The saved game version should not matter, since this is the first time you are entering the Dark Forest - it is not a case of the relevant files not being saved (black map bug), but the default files not being loaded properly in the first place.
It sounds like you have not been to the Dark Forest before at all, but two people in the old forum ran into a similar problem in their second game, where areas cleared in the first game were revealed in the second, and some quest items were missing. Many people have played multiple games, sometimes concurrently, without a problem.
