When I load the ePub file created by Sigil 3.4, it looks beautiful in Sigil 4.0. Just the way you describe.
There are four images in the html which load to images as shown in images.jpg.
The screwed-up TOC is shown in toc.jpg.
I pre-edit the HTML file using EditPadPro. There I insert sigil chapter breaks and the cover and title page and other images. Immediately after loading to Sigil, I press F6 (Split on SGF Chapter Markers) and move on from there.
Could there be something in the html file causing problems???