It seems that a small modification to the definition of ContT can 
restore polymophism:

module ContT (M : Monad) = struct
  type res = unit
  type ('a,'b) k = Cont of (('a -> 'b m) -> 'b m)
  and 'a m = (res * ('a,res) k M.m) M.m

  let return a = Cont (fun c -> c a)
  let bind m k = Cont (fun c ->
    let (Cont m')  = m   in m' (fun a ->
    let (Cont ka') = k a in ka' c))
end;;

The main change is that to have 2 type parameters in your 
continuation.   Also note that while 'a m is defined in terms of res (ie 
unit) for its second parameter, we know this doesn't matter (since 
continuations never really "return"), and thus ocaml is able to infer a 
polymorphic type for bind:

val bind : ('a, 'b) k -> ('a -> ('c, 'b) k) -> ('c, 'b) k

Jacques