Here is a patch that should fix this bug.  Can somebody test that it fixes it?

Thanks,
Sebastian
Index: tree-loop-linear.c
===================================================================
--- tree-loop-linear.c	(revision 140668)
+++ tree-loop-linear.c	(working copy)
@@ -333,11 +333,16 @@ linear_transform_loops (void)
       lambda_loopnest before, after;
       lambda_trans_matrix trans;
       struct obstack lambda_obstack;
+      struct loop *loop;
+      VEC(loop_p,heap) *nest = VEC_alloc (loop_p, heap, 3);
 
       depth = perfect_loop_nest_depth (loop_nest);
       if (depth == 0)
 	continue;
 
+      for (loop = loop_nest; loop; loop = loop->inner)
+	VEC_safe_push (loop_p, heap, nest, loop);
+
       gcc_obstack_init (&lambda_obstack);
       VEC_truncate (tree, oldivs, 0);
       VEC_truncate (tree, invariants, 0);
@@ -350,8 +355,7 @@ linear_transform_loops (void)
 	goto free_and_continue;
       
       lambda_collect_parameters (datarefs, &lambda_parameters);
-      if (!lambda_compute_access_matrices (datarefs, lambda_parameters,
-					   loop_nest->num))
+      if (!lambda_compute_access_matrices (datarefs, lambda_parameters, nest))
 	goto free_and_continue;
 
       if (dump_file && (dump_flags & TDF_DETAILS))
@@ -410,6 +414,7 @@ linear_transform_loops (void)
       obstack_free (&lambda_obstack, NULL);
       free_dependence_relations (dependence_relations);
       free_data_refs (datarefs);
+      VEC_free (loop_p, heap, nest);
     }
 
   for (i = 0; VEC_iterate (gimple, remove_ivs, i, oldiv_stmt); i++)
Index: tree-data-ref.h
===================================================================
--- tree-data-ref.h	(revision 140668)
+++ tree-data-ref.h	(working copy)
@@ -128,13 +128,13 @@ typedef struct scop *scop_p;
 */
 struct access_matrix
 {
-  int loop_nest_num;
+  VEC (loop_p, heap) *loop_nest;
   int nb_induction_vars;
   VEC (tree, heap) *parameters;
   VEC (lambda_vector, heap) *matrix;
 };
 
-#define AM_LOOP_NEST_NUM(M) (M)->loop_nest_num
+#define AM_LOOP_NEST(M) (M)->loop_nest
 #define AM_NB_INDUCTION_VARS(M) (M)->nb_induction_vars
 #define AM_PARAMETERS(M) (M)->parameters
 #define AM_MATRIX(M) (M)->matrix
@@ -149,8 +149,14 @@ struct access_matrix
 static inline int
 am_vector_index_for_loop (struct access_matrix *access_matrix, int loop_num)
 {
-  gcc_assert (loop_num >= AM_LOOP_NEST_NUM (access_matrix));
-  return loop_num - AM_LOOP_NEST_NUM (access_matrix);
+  int i;
+  loop_p l;
+
+  for (i = 0; VEC_iterate (loop_p, AM_LOOP_NEST (access_matrix), i, l); i++)
+    if (l->num == loop_num)
+      return i;
+
+  gcc_unreachable();
 }
 
 int access_matrix_get_index_for_parameter (tree, struct access_matrix *);
@@ -581,7 +587,7 @@ bool lambda_transform_legal_p (lambda_tr
 void lambda_collect_parameters (VEC (data_reference_p, heap) *,
 				VEC (tree, heap) **);
 bool lambda_compute_access_matrices (VEC (data_reference_p, heap) *,
-				     VEC (tree, heap) *, int);
+				     VEC (tree, heap) *, VEC (loop_p, heap) *);
 
 /* In tree-data-ref.c  */
 void split_constant_offset (tree , tree *, tree *);
Index: lambda-code.c
===================================================================
--- lambda-code.c	(revision 140668)
+++ lambda-code.c	(working copy)
@@ -2786,17 +2786,15 @@ av_for_af (tree access_fun, lambda_vecto
 
 static bool
 build_access_matrix (data_reference_p data_reference,
-		     VEC (tree, heap) *parameters, int loop_nest_num)
+		     VEC (tree, heap) *parameters, VEC (loop_p, heap) *nest)
 {
   struct access_matrix *am = GGC_NEW (struct access_matrix);
   unsigned i, ndim = DR_NUM_DIMENSIONS (data_reference);
-  struct loop *loop = gimple_bb (DR_STMT (data_reference))->loop_father;
-  struct loop *loop_nest = get_loop (loop_nest_num);
-  unsigned nivs = loop_depth (loop) - loop_depth (loop_nest) + 1;
+  unsigned nivs = VEC_length (loop_p, nest);
   unsigned lambda_nb_columns;
   lambda_vector_vec_p matrix;
 
-  AM_LOOP_NEST_NUM (am) = loop_nest_num;
+  AM_LOOP_NEST (am) = nest;
   AM_NB_INDUCTION_VARS (am) = nivs;
   AM_PARAMETERS (am) = parameters;
 
@@ -2824,13 +2822,13 @@ build_access_matrix (data_reference_p da
 bool
 lambda_compute_access_matrices (VEC (data_reference_p, heap) *datarefs,
 				VEC (tree, heap) *parameters,
-				int loop_nest_num)
+				VEC (loop_p, heap) *nest)
 {
   data_reference_p dataref;
   unsigned ix;
 
   for (ix = 0; VEC_iterate (data_reference_p, datarefs, ix, dataref); ix++)
-    if (!build_access_matrix (dataref, parameters, loop_nest_num))
+    if (!build_access_matrix (dataref, parameters, nest))
       return false;
 
   return true;

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