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Well, I'm not sure exactly what of part of the installation caused it, but I was trying to install the new version on top of my old one to hopefully keep the database. A lot of it showed up as files in the library, and I could see the folders in admin, but I couldn't see anything in flat view in the library. 


 I ended up uninstalling version 8 of java, so only 17 was installed. Then I installed a copy of 3.0.1 in it's own folder and ran a quick test on some small media sets with the new book/comic/magazine identifiers. It all worked correctly that time.  

Sooo... I'm going to rescan the library because from what I've seen, I really like this new version and it's worth letting it scan for a while. 

Now to find out if Kuboo still plays nice with it.