It may have been an old version I tried, but I was singularly unimpressed by Calibre.
It silently failed to convert some files, plus it insisted on copying every file I opened with it to its own directory.
For its intended purpose (ebook library management for use with your reading devices), calibre is simply the best software out there IMNSHO, paid or not. There are things for which it is not as good, but for my library of epub/kindle ebooks I haven't found anything that comes close. It might not be for you after all, but I'd advice you to give it another try, keeping the following in mind:
The "copying files" thing can be counterintuitive if you're used to micromanage files and folders yourself, but it can be viewed from another perspective: calibre doesn't manage files, it manages *books*. It keeps them in its internal database, of which the folder structure and data files is essentially just the bulk storage part. The files are a subset of all the information that makes up a book record, and the paths are not even used for metadata storage, although it reflects them. I keep a copy of my original files for backup purposes, but they are effectively obsoleted as soon as I clean up metadata and formatting in calibre. After that calibre is the absolutely best way to manage and access my books, and I'm happy to keep them in the calibre "db". After all, a file path is not a good place to store metadata. A db with proper fields, tags and so on is far better suited. Work with it, not against it :)
If you find that it doesn't suit you after some time, the export functionality is excellent. You also have all metadata stored in a well-structured SQLite db to extract and do with as you please.
The conversion error, BTW, is unfamiliar to me. If it simply omitted converting without throwing an error, that's a strange bug I haven't encountered or even heard of. If the results are not satisfactory: be aware that automatic document conversion between some formats, for instance from PDF to a flowing format, is *hard* to perfect, if not impossible. Most of my conversions are between flowing formats, and calibre does an admirable job with those. It even works around limitations in the different formats (by generating a html TOC for formats that don't support proper metadata TOCs, for instance).
It is extremely flexible and extensible. Incidentally the custom column system has a surprisingly powerful template language written by Charles Haley, one of the original authors of ex (which became vi) :)
calibre has a lot of "power user" features built in, a great plugin system with lots of available plugins, and it is very mature at this point. The relevant sub-forum at MobileRead is an excellent resource, any questions you might have are most likely already answered there.