Give this a whirl:

{-# LANGUAGE TypeFamilies,TemplateHaskell #-}
module Bug where

    class C a where
        type T a

    $([d|  
        instance C (Maybe a) where
            type T (Maybe a) = Char
        |])

$ ghc -c Bug.hs 
Loading package ghc-prim ... linking ... done.
Loading package integer-gmp ... linking ... done.
Loading package base ... linking ... done.
Loading package ffi-1.0 ... linking ... done.
Loading package array-0.3.0.0 ... linking ... done.
Loading package containers-0.3.0.0 ... linking ... done.
Loading package pretty-1.0.1.1 ... linking ... done.
Loading package template-haskell ... linking ... done.

Bug.hs:7:6:
    Type indexes must match class instance head
    Found `Maybe a[aMy]' but expected `Maybe a[aMx]'
    In the associated type instance for `T'
    In the instance declaration for `C (Maybe a[aMx])'
[glastonbury:~/Projects/Haskell/Truth/Core]$