You're probably just getting unlucky. Do you have the "Special Promise" divinity activated? If so and you still aren't getting a bonus stage after 8 or more hours offline, then that's most likely a bug.
Until proven otherwise, this is a certified 
moment
#I'm Stuck - Bonus stage boxes NEVER spawning
flint pendant
you had a what on overnight? 
raven fable
DIE TRAITOR
flint pendant
flint pendant
~~the autoclicker may have made it so you don't jump high enough to hit boxes~~
yeah. Vertical magnet screwed him over
flint pendant
~~the autoclicker may have made it so you don't jump high enough to hit boxes~~
^^
You're using an autoclicker anyways, so you don't deserve good luck
viscid merlin
Idk, I get one every 5-10mins
flint pendant
that's with maximum random box spawn speed, as well as the +3% chance of getting one
cerulean wolf
I have the same problem. Since the AoT update I think I havent got any bonus level box
normal perch
play more, its random
normal perch
its random, nothing has changed
did you cheat? are you playing offline? there's nothing else that will affect the chance of special random boxes spawning
plain rampart
@cerulean wolf do you have the divinity that gives you 100% chance for BS if you haven't logged on for 8h ? If so, does it work ?
cerulean wolf
i haven’t unlocked divinities yet
plain rampart
arf
normal perch
It’s 5% chance for each random box to be a special random box