I think he put that in his journal because of the experience with Desmond in the past to act as a saftey, but I don't think he's jumping back and forth in time. If he was, he would be passed out in the "present" time at least once in a while.
However, I do think that he will go through the same time jumping thing at some point. Remember how he was crying in his flashback when they found the remains of the flight on TV? And he didn't know why he was crying? I wonder if this is him travelling back in time and suffering the same problem, but he won't be able to find Desmond.