After a little over 12 days of in-game play time, I'm having a lot of trouble with Refined Storage.
It's become impossible to extract items manually from the system. Whether it be from using a grid or a wireless grid.
I can still export items from the system using an exporter and I can still craft using the crafting grid.
Whenever an item or fluid is imported into the system and I am using a grid, the items/fluids will be imported into their own stack of item/fluid without stacking with the already present ones. Once the grid is closed and reopened, the items/fluids will have stacked.

I'm also having some trouble with TPS spikes from time which might be linked to the problem I'm having But I'm unable to determine the source of those.

Is the storage your Refined Storage system is using on a Refined Storage disk, external (attached to Refined Storage via an External Storage), or both?

It's using both the disk from Refined Storage, from Extra Storage and also multiples external storages connected to a Functional Storage controller and multiple fluid tanks.

What is even stranger is that if I let the game run without touching it for a few hours, the problem goes away...