While 1.0.2 fixes pretty much all the bugs that were discovered since the v1.0.0 release, it also has an unfortunate side effect. Prior to 1.0.2, the save file had a bug which cause the overlapping of the main game saves with the custom level list, resulting in corruption and possible crashing of the program with an error. The problem is fixed in v1.0.2, but it also caused saves from pre-1.0.2 to not be compatible (in the sense that the program may crash). You will have to delete the MM2PTCSV file from the MEM section so that it may create a new save upon launching. Some may feel confident enough to alter the save to try and preserve the data, but as was said, it’s likely that the main game save or level list is corrupt, so some data is already lost.
Sorry for the inconvenience.