The same thing is happening to me. I wrote about it on the Beamdog forum some time ago.
https://forums.beamdog.com/discussion/comment/1062026#Comment_1062026
At the beginning of the game underground. When I come across gnomes and kill them, a conversation with Imoen takes place. Immediately after the interview, two identical entries appear in the journal. As shown in the picture from the attached link. Can anyone advise where the mistake is. This does not happen in the basic diary of the game.