There is an issue with the Virtex-6 FPGA DDR2/DDR3 read leveling algorithm, which affects ALL designs using x4 parts.
This causes problems in hardware where any nibble beyond DQS[0] either does not calibrate correctly, or does not finish calibration. This issue is seen in simulation onlyif calibration for all bytes is enabled (i.e., SIM_CAL_OPTION = "NONE").