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The mismatch in scores could be because the scores in the training log are updated after each batch.
history.history scores match the scores in the CSV, the loss and metrics you get from history.history are averages over epoch. I've provided validation data and run your code in this gist and it seems to work.
Basically two issue.
Training log says, for first epoch acc: 0.83 but in csv, it is .90. Also with the loss scores.
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