This is because when SIM_BYPASS_INIT_CAL = "OFF" in sim_tb_top, the read leveling algorithm does multiple iterations and applies the averaged results, which is impractical to run in simulation. This setting is intended for hardware implementations only.
To see the complete calibration sequence in simulation, except for the multiple read leveling iterations, set the following:
SIM_BYPASS_INIT_CAL = "OFF" in sim_tb_top
SIM_CAL_OPTION = "FAST_WIN_DETECT" in phy_top module
This will be included in the 13.4 Virtex-6 FPGA Memory Interface Solutions User Guide (UG406).