I was using the All the Mods 7 (version 0.3.21 since that's the one with the server) and added Rubidium, Rubidium Extras, and Oculus so I could use shaders.

When I first launched the game, it worked fine then suddenly the items don't show up anymore. They're there since I can click and see the recipes and show up when I type in specific items or search via mods.

That’s a feature of Rubidium Extras. It hides items from JEI until you search. You can disable this in the config.