Hierarchical netlist does not link correctly in Primetime

This is a new problem resulting from fixing the problems in this thread.

i have all of these names n?? and U?? in my netlist, the question is when i apply top-down approach for syntheses i didn't had these problems , how can hierarchy names have changes when i change my synthesis method ??

the whole error message is as follow:
read_ddc ./out/Sbox.ddc
1
read_sdc ./out/Sbox.sdc
Loading db file '/root/Desktop/Dpa_V2/db/NangateOpenCellLibrary_45nm.db'
Linking design Sbox_1...
Warning: Unable to resolve reference to 'lookup' in 'Sbox_1'. (LNK-005)
Warning: Unable to resolve reference to 'regOut' in 'Sbox_1'. (LNK-005)
Creating black box for ins_regout/regOut...
Creating black box for ins_lookup/lookup...
Information: Removing 5 unneeded designs..... (LNK-034)
Information: 134 (100.00%) library cells are unused in library NangateOpenCellLibrary.....
Information: total 134 library cells are unused.
Information: Issuing set_operating_conditions for setting analysis mode on_chip_variation. (PTE-037)
set_operating_conditions -analysis_type on_chip_variation -library [get_libs {NangateOpenCellLibrary_45nm.db:NangateOpenCellLibrary}]

Reading SDC version 1.8...
1
read_parasitics ./out/Sbox.spef
Information: Derived library resistance unit is 1.000000 Kohm (Time unit is 1 ns, and Capacitance unit is 1.000000 pF). (DES-028)
Error: Cannot find port/pin 'ins_lookup/U675/A1' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U695/A1' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U721/A2' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U811/A2' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U861/A2' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U872/A1' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U775/A1' in design 'Sbox_1' (DES-002)
Error: Cannot find port/pin 'ins_lookup/U740/A1' in design 'Sbox_1' (DES-002)
...
Error: Could not resolve net 'ins_lookup/n1324'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n1325'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n1326'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n1327'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n1328'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n1'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n2'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n3'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n4'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n5'. (PARA-075)
Error: Could not resolve net 'ins_lookup/n6'. (PARA-075)
Error: Could not resolve net 'ins_regout/N3'. (PARA-075)
Error: Could not resolve net 'ins_regout/N4'. (PARA-075)
Error: Could not resolve net 'ins_regout/N5'. (PARA-075)
Error: Could not resolve net 'ins_regout/N6'. (PARA-075)
Error: Could not resolve net 'ins_regout/N7'. (PARA-075)
Error: Could not resolve net 'ins_regout/N8'. (PARA-075)
Error: Could not resolve net 'ins_regout/N9'. (PARA-075)
Error: Could not resolve net 'ins_regout/N10'. (PARA-075)
Error: Could not resolve net 'ins_regout/n9'. (PARA-075)

****************************************
Report : read_parasitics /root/Desktop/Dpa_V2/out/Sbox.spef
Design : Sbox_1
Version: D-2009.12-SP3
Date : Thu Jul 9 14:37:18 2015
****************************************

617 error(s)
Format is SPEF
Annotated nets : 26
Annotated capacitances : 0
Annotated resistances : 0
Reduced coupling capacitances : 0
Annotated PI models : 10
Annotated Elmore delays : 0

why prime time could not link sub modules regOut and lookup as marked above ????