I am seeing similar FC errors with Sigil 0.4-RC1 when I create new files by splitting one large file into several chapters. In my case, all the files are physically present in the epub archive, but several are not listed in the manifest or spine sections of the content.opf file. That, and the order of files in the spine is munged up too.
That's what I think FC means when it says something to the effect that "such-and-such.xhtml is reachable but not listed in the <manifest>" etc.
So my guess is that for some reason RC1 is not properly updating the content.opf file.
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