It sounds like you have portions of the 0.9.5 version supplied by the standard repositories and my much older 0.8.6 standalone package. If you're seeing 0.9.5 in the about dialog, though, then that's certainly the version you're using.
If you launch Sigil and open the preferences dialog, you'll see a button that will open the preferences directory in a file browser. I don't remember the path exactly off the top of my head, but I know it starts with ~/.local.
If you want the latest version of Sigil (v0.9.8), I'd remove both the repo-supplied version and my older .deb version and use the standalone installer I created for 0.9.8. More info can be found
here.