I have a Controller connected to my Refined Storage system via External Storage bus (priority is set to higher than everything) and just a bunch of Drawers around the Controller all connected. I pick a random drawer and put some cobblestone in it. All cobblestone I put in my refined storage should go into this drawer now. If I right click on the controller with cobblestone, it goes into the proper drawer. But if I add cobblestone through the Refined Storage grid, the cobblestone goes to the first open drawer in the system and not into the drawer that already has cobblestone in it. If I add more cobblestone through refined storage, it goes to the most recent drawer. It doesn't put it in an 3rd drawer.

I've tried tearing down the whole thing and rebuilding it. I've tried locking the drawer. Chunkloading all the chunks around it and about a million other things. I've asked around on my server and it seems to be working fine for them. Just I am having the issue.

Lock all drawers that you have connected to the Controller, that way the only proper destination is the drawer with cobblestone already in it.

It should still give priority to drawers with items in it over drawers that are empty. If RS is walking the slots itself or doing some form of caching though, I can't be sure it's respecting the order.