I have tried my best trying to figure out what is wrong but I could not get the solution. The description is in the pdf. Thank you for your help. I would be happy to learn from it.

 

I dont see the need for the timer based on the problem specs.
It would seem to me you want the conveyor to run any time the Proximity switch is not made or (it is made and the level switch is made) (saying the box is full) . There may be a timing issue there between the time the proximity switch doesnt see the box in place anymore and the level switch still seeing the full box. You might need a small off delay timer. Good luck and have fun thinking it through

 

I also noticed in the control logic, the WALNUT BIT SW is B3:07 and in the I/O you have it controlled by B3:05.
Looks like an error to me.

 

It is hard to tell without knowing what exactly isn't working. If the logic just isn't doing what you think, I would remove timers, unless used as a failsafe.

Your writeup mentions using level switches to determine when full and to start the conveyor again.

Since you have a sensor for the level, a timer seems to be redundant and could be messing with your logic.

If you're concerned about a sensor failing and overfilling, you could always add a timer like, "if filling begins and level switch doesn't close after X seconds, close a switch to turn the conveyor on and sound alarm" - or something like that. This way the process isn't being controlled by timers, but you have visibility into any issues.

But since you seem to have sensors for each step, timers in the process itsslf seem like a waste here.

Hope that helps?!