I have craftbukkit.jar 1.3.2 R1.0, and sometimes, people try to craft something, but nothing appear in the right square (sent you a picture below). It vary with people and reload (almost random) I touched nothing before the problem. Tried to redownload build, but didn't work...
There is some picture that could be helpful: As you can see, there is a -1 after each bugged items. (unworking item was got legitimatly, normal item with TMI)
first time i see a negative metadata item.. odd. do you have any other plugin that can get metadata info? (essentials/worldedit) if yes, try check the item with them aswell.
List of ALL my plugins: AutoGamemode, Automessage, Bedspawn, Bookswithoutborders, BOSEconomy, bPermissions (well-set), Buttoncommand, Chestshop, Citizens, copybooks, firstjoinplus, Halloweenscares, iConomy, iRules, Lockette, Magicspells, MCVote, Minebackup. mobcatcher, Multi-inv, Multiverse-core, Quests, Realmodt, simpleprefix, Travelgate, Vault, WorldEdit, WorldGuard, xAuth (easiest password plugin)