@Katsunami: If you are trying to replace a file, use replace file, not add file. And there was a bug in replace file that caused an error when replacing files with the same name, now fixed.
https://bugs.launchpad.net/calibre/+bug/1260822
@eschwartz: Yes importing HTML/CSS files is currently broken (always results in a blank file), just use copy paste, fix will be in the next release.
Also please open a bug report for the toc move feature, or I might forget. Right now there is a whole deluge of small things to be fixed/changed/added to edit book.