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My guess would be you are not running ebook-convert directly but through a BAT file. That would result in the behavior you describe.
Even if it is not the case, the fix that would have worked with BAT files will likely work for your case: Just prefix your calls to ebook-convert with either call or cmd /c. Unlike the start fix, this will NOT start a new console window for each ebook-convert, and it will run te commands sequentially rather than all at once.
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