The problem is in the calibre conversion code. For everything except epubs, the conversion process strips the ToC entry pointing to the cover before passing everything to the output plugin. I have made a change to add kepub to the exceptions and checked it in. Assuming Kovid agrees, it will be in the next release.
For those who want to check, the change is
https://github.com/davidfor/calibre/...fd85fbb5bf941e