Windows MobiPocket Reader does not go a very good job on ePub to MOBI conversion, it does not convert the table of contents for example, but it may be good enough.
Generally a better bet is Calibre (it has its own forum here), which has excellent conversion from ePub to MOBI and the Calibre team will actually fix bugs (MobiPocket has an incredibly long development cycle). I use Calibre's command line tools (oeb2mobi or any2mobi), but the GUI will also work.
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