Not sure if it's related to this issue, but there was this was committed (added "Start with Favorites")
https://github.com/koreader/koreader/pull/6577
Probably not related, since the initial problem was in March but just in case. Side-note I tested it on 3 different devices and can't reproduce at all (didn't test it on Kindle, since I factory reset it without knowing USB is broken
)