:- use_module(library(clpfd)).

  rle([], []).
  rle([H],[[H, 1]]).
  rle([H | T], [[H, CountPlus1] | More]) :-
      Count #> 0,
      CountPlus1 #= Count+1,
      rle(T, [[H, Count] | More]).
  rle([H | T], [[H, 1], [Element, Count] | More]) :-
      Count #> 0,
      dif(Element, H),
      rle(T, [[Element, Count] | More]).

Even though I'm the one who was making the execution model complaint, this implementation seems to work for me.

  ?- rle([1,1,1,2,3,1,1],X), rle(Y, X).
  X = [[1, 3], [2, 1], [3, 1], [1, 2]],
  Y = [1, 1, 1, 2, 3, 1, 1] ;
  false.