Forge: 1291
AgriCraft: 1.3.0 alpha 3 (from curseforge)

After using Quadrum to make a custom item and setting it as the fruit for a custom crop, the journal instead uses the missing-texture icon instead of the actual one. All of the other textures render just fine, both in-journal and in-game, and the custom item shows the right texture in NEI and my inventory. Could it possibly be caused by Quadrum storing its textures in its config folder?

That's most definatly it, I'll use a different method to render items in the journal. When I wrote that journal code I wasn't aware of certain methods in the Gui class, however I'm aware of those now. It'll simplify things a lot.
For now, all you can do is make a resource pack and put that texture in it, my apologies