If it helps, it appears to happen most often when I’m in the “All” tab when either system messages are generated or I receive a whisper from an ongoing conversation (new whispers pull you to the whisper pane but ongoing keep you in “All”).
From what I’ve seen when it happens there seems to be a padding issue between messages. I’ll start to get larger and larger gaps between messages instead of a static padding between displayed messages. And then ■■■■ hits the fan quick-style XD
Does not appear dependent of the presence of the time stamp (seen in screenshots) but I cannot confirm if changing the text size had anything to do with it or not. (side note on a minor bug: changing text size does not update the displayed number on the slider in the /lkc setting until after closing and reopening the pane)