• Daniel received the journal from a future and more experienced version of himself.
• Daniel and the rest of those that stayed on the island stopped skipping through time when Jack and crew returned to the island via flight 316. Daniel got himself recruited as a workman (as seen in the opening scene of Season 5). According to how Lost treats causality, sometime after he sees the Orchid station, Daniel would have hidden the journal right where he found it in the 'future' (past to him), then he would have to begin writing the journal anew so that it could be written in the first place.
• Daniel's journal will eventually become known as the Black Rock Ledger

Journal Time-loop TheoryEdit

• The Journal is in a time loop. Daniel adds new things to it every loop, and his memory problems exist to prevent him from knowing the future. Eventually (possibly what we are seeing in the show), the information in the journal will end the time loop.
  • This is the theory I too have been toying with... When Daniel first received the journal, it was empty (or at least sparse). Every time it goes round the loop, Daniel adds to it. What we are seeing is the last loop, where the journal contains enough info for Daniel to 'solve' the loop. This is suggested at by Jacob in The Incident, Part 1 when he says "It only ends once..." Each loop, many events are the same (constants), due to the universe "course correcting", but the details in between, and the people involved are different each time (variables).
  • Also, Daniels experiments on himself may have given him ALL the memories from ALL the loops, therefore making him seem confused and mad. He doesn't want to tell anyone in the real world as he would get locked away, but once he is on the Island, it all makes more sense to him.
  • Expanding this more, I expect Daniel to turn up in the alt. timeline expecting for the plane to have crashed.