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I have the same issue with 2 journals that are in my log (Mira's Letter and Gravedigger's Log) but not listed under their achievements (A Quick Study and Historian of Tristram respectively). I also didn't get credit for The Shattered Crown quest so this must have all happened right before a server crash. I was able to redo the quest but of course the books don't drop anymore.
Right now the solution appears to be that the journals can be reclaimed with a hardcore character. Fortunately the ones I'm missing are early in the game but others may not be so lucky.
There is some more discussion about this issue in another thread located here:
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