Items named in an anvil don't stack with other items with another of the same name (named separately)

I'm naming filler items for a sorting system on a server, and whenever I name a stack of stone, it works fine until i split it up into another stack and then try adding other items to one of those stacks that has the same name.

It seems to be random whether or not a certain stack can combine with another.

I try to combine two stacks and they seem to do so until I exit the inventory or interact with another item. It then moves to another slot as if it never did combine. This hints to me that it's a problem between the client and the server, but I can't say for certain.

To reproduce:
1. Name a stack of stone (not a full stack) to "A"
2. Name another (not full) stack of stone to "A"
3. Try combining the two stacks