Comparators need to be broken and replaced upon entering the realm in order for them to work correctly. 

Not correctly locking for filtering items. 

1. Create filter system using comparator and hoppers.
2. Put 41 of the stackable item you want sorted into the first slot of the hopper.
3. Put 4 different blocks into the other 4 slots.

Should lock the hopper to items not of the same type as the 41 items. 

Result: nothing is filtered. All items drain out of the hopper.