Ok, I have found something. If you change the first 'if(x)' to 'if(!x)' in the loop after the load_all_plugins call in uds::PluginMgr::create_document you can load all files (tested mobipocket, pdf, djvu) correctly. (I don't have the source code, so it might look a little different of course
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I'm not sure if this is the real problem or that it's just a coincidence that this change just makes it work.