I'm guessing you're currently starting KOReader from a non-standard orientation (I take the standard "Portrait" to be Portrait, buttons on the right, FWIW).
That will indeed result in fun rotation shenanigans, for
a very stupid reason 
.
(i.e., we do nothing instead of enforcing Portrait on startup).
The fix hasn't yet hit a nightly, but I'll get it in the day after tomorrow at worst.
In the meantime, things *should* behave as long as you're launching KOReader with Nickel in Portrait (provided Nickel doesn't decide to rotate on open ;p).