Adzim,
In looking at the qsf from your *.qar file, there are a number of nibbles that aren't contained in a nibble, they cross the nibble boundary (they stay in the byte).
Example:
set_location_assignment PIN_LH42 -to emif_mem_mem_dq[71]
set_location_assignment PIN_LL43 -to emif_mem_mem_dq[70]
set_location_assignment PIN_LL39 -to emif_mem_mem_dq[68]
set_location_assignment PIN_KW43 -to emif_mem_mem_dq[69]
set_location_assignment PIN_KW41 -to emif_mem_mem_dqs_n[17]
set_location_assignment PIN_LB40 -to emif_mem_mem_dqs[17]
set_location_assignment PIN_MA34 -to emif_mem_mem_dqs_n[8]
set_location_assignment PIN_LW33 -to emif_mem_mem_dqs[8]
set_location_assignment PIN_KW39 -to emif_mem_mem_dq[65]
set_location_assignment PIN_LB38 -to emif_mem_mem_dq[64]
set_location_assignment PIN_LB42 -to emif_mem_mem_dq[66]
set_location_assignment PIN_LH38 -to emif_mem_mem_dq[67]
LL39 is in DQ44, while LH42, LL43, and KW43 are in DQ45.
How did you generate this pinout for the EMIF? And what is wrong with the one we generated? If I don't know what is wrong I can't fix it on other EMIF interfaces.