I've managed to recreate the bug, from what I can see it only occurs if the battle wait mode is set to Full. Changing the wait mode should fix it, battle settings can be changed in the System menu. I will work on a fix for this for all wait modes in the mean time. I apologize for any inconvenience this may have caused. Thank you for bringing this to my attention, and I hope you'll continue to play.
EDIT: I've found a way to fix the bug on all wait modes, I'll be releasing an updated version with the bug fix within the next 24 hours. Thank you for your patience.