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Minecraft version: 1.12.2

Wizardry version: 4.3.4
Environment: Server

Issue details: Unable to craft magical crystals from crystal flowers

Other mods involved:

I checked and no it wasnt witchery resurrected

I'd suggest joining the discord server to have a quicker way to discuss, you can find the link in the mod's CurseForge page.
Otherwise, what does JEI show for the Crystal Flower? No recipes at all?

Very strange, since that recipe is entirely handled by the vanilla system and wizardry only provides the JSON file for it. What crafting interface are you using, the vanilla workbench, the 2x2 grid or a modded crafting table?