It's hard to blame it all on the publishers. Some of it definitely depending on what complaints one has, but it's usually the distributor who makes the individual formats. But yes, I'm sure none of the publishers have what one would call an optimal work-flow in place yet.
Take Hachette (Orbit, etc.) for example. They send out an ePub to distributors (not sure if it's generated from InDesign or what). It's then up to distributors to make whatever formats they plan to offer from that. So if it's a certain format that has a problem it's likely whatever conversion the distro made (and probably didn't proof well). Of course it's the publisher's "fault" for doing things this way I suppose.
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