Stripping everything but the $scope-$upscope heirarchy....there seems to be a problem with your output.
Code:
$scope module testbench $end
$scope module uut $end
$scope module mc8051 $end
$scope begin \gen_mc8051_siu(0)\ $end
$scope module i_mc8051_siu $end
$upscope $end
$upscope $end
$scope begin \gen_mc8051_tmrctr(0)\ $end
$scope module i_mc8051_tmrctr $end
$upscope $end
$upscope $end
$scope module i_mc8051_control $end
$upscope $end
$scope module i_control_mem $end
$scope begin \for_tmr(0)\ $end
$upscope $end
$scope begin \for_siu(0)\ $end
$upscope $end
$scope begin \for_intext_edge(0)\ $end
$upscope $end
$scope begin \for_tf_edge(0)\ $end
$upscope $end
$scope begin \for_siu_edge(0)\ $end
$upscope $end
$upscope $end
$upscope $end
$scope module i_mc8051_alu $end
$scope begin gen_multiplier1 $end
$scope module i_comb_mltplr $end
$upscope $end
$upscope $end
$scope begin gen_divider1 $end
$scope module i_comb_divider $end
$upscope $end
$upscope $end
$scope begin gen_dcml_adj1 $end
$scope module i_dcml_adjust $end
$upscope $end
$upscope $end
$scope module i_alumux $end
$upscope $end
$scope module i_alucore $end
$upscope $end
$scope module i_addsub_core $end
$scope begin gen_greater_four $end
$scope begin \gen_addsub(1)\ $end
$upscope $end
$scope begin \gen_addsub(2)\ $end
$upscope $end
$scope begin \gen_addsub(3)\ $end
$upscope $end
$scope begin \gen_addsub(4)\ $end
$scope begin gen_nibble_addsub $end
$scope module i_addsub_cy $end
$upscope $end
$upscope $end
$upscope $end
$scope begin \gen_addsub(5)\ $end
$scope begin gen_last_addsub $end
$scope module i_addsub_ovcy $end
$scope begin gen_greater_one $end
$upscope $end
$upscope $end
$upscope $end
$upscope $end
$scope begin \gen_addsub(6)\ $end
$upscope $end
$scope begin \gen_addsub(7)\ $end
$upscope $end
$scope begin \gen_addsub(8)\ $end
$upscope $end
$upscope $end
$upscope $end
$upscope $end
$upscope $end
$scope module Interal_RAM $end
$scope module U0 $end
$scope begin no_input_stage $end
$upscope $end
$scope begin native_mem_module $end
$scope module mem_module $end
$scope begin async_coll $end
$upscope $end
$scope module reg_a $end
There seems to be a bunch of missing $upscope to for the previous $scope starting at Interal_RAM. See post #2