This problem was indeed caused by the epub reader setting the line height in em units. I have found a patch that fixes the problem by making the epub reader use a unitless line height, the same way the kepub reader does.
I've attached a test epub that demonstrates the problem, and screenshots showing the epub at the same line spacing setting without and with the patch.
(See these threads in the developer's forum for patching
firmware 3.1.1 and
firmware 3.2.0.)