This is just the way the KePub reader works (the ePub reader works differently though). If you select publisher default you get the embedded fonts. If you select any other font, that selection overrides everything in the KePub.
There is a
firmware patch that can change this behaviour, named `Un-Force user font-family in KePubs`.
Edit: To see the diference between how the KePub and ePub readers work, these are the respective sections of the built-in stylesheet that are activated when you select a font other than "Publisher default" from the device's font menu:
ePub reader:
Code:
body, p { font-family: -ua-default !important; }
KePub reader:
Code:
* { font-family: %1 !important; }
where -ua-default and %1 both refer to the selected font.