You're right, I don't think this has been mentioned before. Very strange. It sounds a little bit like the "tiny font" bug of firmware 2.3.1, where with each new chapter the font is suddenly tiny. It goes back to normal after you make the text larger and then smaller again (back to where the slider was). There's a fix for this bug in firmware 2.3.2.
What firmware are you using? It might be fixed by upgrading to 2.3.2 (or downgrading to 2.1.5)... Or as you suggest, it might also go away by using the kepub reader (so changing the .epub extension to .kepub.epub).