Using -Bukkit-1.1-R4-b1938jnks Plugins I am using: PHP: CreeperHeal, PlugMan, XrayInformer, N3W_HardCore, Spout, LogBlockQuestioner, Vault, MCDocs, BorderGuard, StopTalkingAutoBan, CraftIRC, Spectate, WaterproofRedstone, MoreRecipes, iConomy, MachinaCore, boosCooldown, Permissions, BlocksOnGlass, MachinaPump, MachinaBuilder, AcceptRules, N3W_TheEndAgain, ColorMe, FalseBookCore, CommandDisabler, PlayerFreeze, FalseBookCart, MachinaDrill, WorldEdit, PermissionsBukkit, CommandBook, Gold2Economy-Vault, LogBlock, LWC, WorldGuard, dynmap, mChatSuite, Dynmap-WorldGuard, BukkitIRCd, FalseBookIC, FalseBookExtra It started to occur in 1.1. Rarely it is possible to craft Brewing Stand but usually you can't. Recipe is 100% correct but no output (Brewing Stand). By no output I mean this: It doesn't depend on reload or restarting server. No error logs.
Since I have no idea what is wrong, try removing all plugins, and if that fixes it add them back one by one until you find which one stops it.