Every ePub issue I've encountered with Stanza has been caused by calibre's conversion of the ePub. Maybe it's Stanza's bug, that much I don't really care about. The more important thing is that when I took the same files and converted them through stanza deskop, the problems disappeared.
Another alternative is to convert your ePubs to another format and use another reader like BookShelf which is fairly decent.
It's too bad you can't put your own books in the Kobo reader.
Also it's too bad stanza is the only decent reader app on iPhone because after iBooks is public, Amazon will probably become more aggressive vs. Apple, and there could be a decent chance of Stanza development being stopped permanently :-/ (Just speculation of course.)
It would be nice if Bookshelf would implement ePub support, because, otherwise it's one of the better alternatives to Stanza.
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