What @davidfor said.
The kepub override CSS file contains:
Code:
div, p { text-align: %1 !important; }
so if you set the [Aa] menu's Justification button to anything other than 'Off' your screenshots are what I'd expect to see.
Your best bet is to enable the kobopatch 'Un-Force user text-align in div,p tags in KePubs' so that the kepub override CSS will be like the epub override CSS.