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I think there is a more generic problem in that if you convert multiple books, some of them can be left in that state. In particular in my experience this tends to happen if there are any errors reported during conversion. I simply remove them and re-add them for converting. I have not spotted a specific pattern that tells you in advance when that specific books will be left in this state.
I think Kovid has said elsewhere that this problem will not fixed until he has a chance to rewrite the whole job management sub-system.
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