If you were a scientist conducting time travel experiments or, as Faraday said, "This is when I do what Oxford frowns upon," don't you think you would eventually have to try the experiment on yourself? It's not like there a volunteers and every "mad scientist" eventually uses himself as a test subject (see The Fly, The Prestige, The Invisible Man) I think this is excellent proof that Daniel is also unstuck in time, as he called it.

Not sure if he has existing memory problems (he seemed a bit squirrelly in the flashback) or if it a result of the time travel process but I'm willing to bet its from the time travel. He just forgot about meeting Desmond all those years ago and writing that note in his book.