In the latest version you can no longer craft chests out of the wood tag meaning that you cannot craft a chest out of modded wood unless the mod defines a recipe for a chest, you can still craft chests out of vanilla wood because of the quark recipes.

I too have this issue.Also cannot craft a vanilla chest unless you use skyroot planks from The Aether mod as that is the only recipe. Trying to use any other vanilla wood will only make Quark Chests which you can convert to vanilla, but thats an extra unnecessary step imo. I don't want to have to use two patterns in Refined Storage just to make a vanilla chest, when just one should suffice. (I prefer the look of vanilla chests over quark ones)
Edit: actually refined storage wont let me make a pattern to convert the Quark Chest to the Vanilla One. When I click the alternate pattern button and choose the Vanilla Chest, then click the arrow to make the pattern, it just makes a Functional Storage Oak Drawer pattern instead.

This should be resolved next update. The quark config has been amended to disable the quark chests.

The Quark chests are used in the FairyTale MineColonies style (from StyleColonies), which makes some buildings impossible to complete. Perhaps there should be a specific recipe added for the Quark chests so they don't block that style.