It is already reported issue:
https://github.com/koreader/koreader/issues/2314
It looks that cause of the problem is updating koreader through OTA service and not using PC uploaded version you can find here:
http://build.koreader.rocks/download/nightly/
From people's comments full downloads work fine, but something went wrong with OTA servers. Hopefully, soon we also will have working OTA updates (without glitches like this).
And also, you now know that it is wise to set at least 1-2 seconds in KSM to choose option other than the one that causes you problem.