There seems to be an issue with the Ender IO filters and gregtech chests with the Existing Item Filter only seems to snap shot the item at the top left of the chest. It makes it extremely difficult to manage the massive inventory necessary for this game.

Does the issue also occur with other chest types like vanilla or Crates?

Yes they seem have the same issue it might be a limitation of ender IO

I'd recommend using gregtech conveyers and oreDict filters for ore processing purposes.

Also it sounds like this is a bug in the current version of EIO from what you're saying.