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I've just read this entire thread, and I'm wondering about the "save to disk" action you keep taking. Is it possible that you've saved into the Calibre library storage folder? My reading of your early explanations suggest this.
When I first started using Calibre I found that option tremendously confusing. It's poorly named -- it's actually an export (copy), for use with non-recognized devices or for other sharing. It seems like it should be a "save my changes" or "update my library" function, but it's not. It can be used to export your entire library filtered to, say, a single format, then reimported back into Calibre after deleting the old library, thus shrinking and simplifying it by removing other conversions or sources.
If you did save into the Calibre library folder, it would explain why you had "quadruples" of folders in the library, all with different folder names.
I think you've moved your library already, but it's also possible that there were naming collisions that corrupted your sources and that permissions were mangled -- and that some of this was carried over to the new location.
Just a thought.
At this stage, I'd do an uninstall and a fresh install with a different library location on a local disk. Then import maybe six or eight books by three or four authors to experiment with so you're not juggling too many variables.
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