The latest versions of eBook Publisher seem to have issues with drag 'n drop after adding files. I need to drop the item one or two entries higher for it to be in the correct spot. I just save the .opf and manually edit it when I can't use eBook Publisher to do it right.
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Gripes about eBook Publisher issues!
Also, in their most recent updates, they don't seem to support Unix "/" in filename paths anymore and only recognize the MS DOS "\" when referred to in href's/links.
It can't compile my large ebook creations of yesteryear whereas v2.2.5 was rock solid.
It has issue opening and resaving the .opf and on many occasions has even refused to reload a .opf it just saved (mind you this happens more when loading and converting older v2.2.5 .opf's)
Oh, well, such is way of legacy device support!!! 
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