My issue was caused by one or two bugs that have been fixed short after. If I remember correctly, one had something do to with the way Calibre output the file. The other I don't know, but I don't have the problem any longer. I didn't do anything to fix it myself.
In earlier versions of Sigil, a file was included that you had to run to install the Visual C++ 6.0 runtime components in Windows. Although it is as far as I know no longer included with Sigil, you could installing that. Perhaps it'll work. See here