Bukkit

They don't work with MultiCommands either. However they do work with SimpleAlias.
It's formatted like this in the config:
market:

    1: /warp market

Other commands with BetterAlias do work. All that happens is "Unknown command" with warps.

It might be a plugin incompatibility.
^^
Plugins (57): WorldBorder, VoidtoSpawn, PluginManager, Vault, ChannelChat, Multiverse-Core, MobBountyReloaded, TreeAssist, SimpleWarnings, AutoMessage, JukeLoop, CFBanner, CedSlap, Votifier, ForcedGrammar, FoundDiamonds, CleanroomGenerator, BetterAlias, WorldEdit, NoCheatPlus, Statues, Multiverse-Inventories, TagAPI, Multiverse-NetherPortals, PermissionsEx, LogBlock, LWC, WorldGuard, DispenserRefill, KeepItems, ItemsForVote, ImgMap, SignEdit, BookManager, mcbans, DailyBonus, GriefPrevention, TheEndAgain, Essentials, CreeperHeal, Multiverse-Portals, MagicSpells, ChestShop, EssentialsChat, GPRealEstate, ChessCraft, EssentialsSpawn, NameTags, VanishNoPacket, IslandWorld, AutoRank, MagicSpellsShop, PayDay, Factions, BattleArena, ArenaPaintball, SimpleAlias
^^

Sorry just noticed this one... I'm not sure what you mean, can you elaborate?

Plugins (13): BetterAlias, CCLogger, PluginManager, HeadNamer, Lockette, PermissionsEx, Multiverse-Core, NullTerrain, Essentials, ChatManager, Multiverse-Portals, Multiverse-Inventories, Multiverse-SignPortals

Those are my plugins and i have no problem using an alias with /warp <warpname>

Brosif, you gotta do 0: And not 1: if you want it to read a one word command. 1: is for when you have just 1 argument. Since something like /market doesn't have any arguments and is simply a one word command, you'd have to do...

market:
   0: /warp market