The default value for PMA_RX_CFG_0 and PMA_RX_CFG_1 for the GTPs generated by IBERT is incorrectly set to 09F0089, and they should be set to 09F0088 for most applications.
Changing the PMA_RX_CFG_0 and PMA_RX_CFG_1 attributes for a tile can be done easily though the use of the "Edit DRP" functionality provided in the IBERT GUI. Once the device is configured and Analyzer has connected to the IBERT design, the IBERT Virtex-5 GTP Console can be brought up by double-clicking on that option in the upper left-hand window of the Analyzer GUI. With the IBERT Console open, the Edit DRP button becomes available on the MGT/IBERT Settings tab.
Once you click the "Edit..." button, a new window will come up allowing you to select and change a particular attribute. Use the drop-down menu to select either "PMA_RX_CFG_0" or "PMA_RX_CFG_1" and verify the current setting of both. The expected default and value that will work best for most designs is "09F0088". For other supported values, please refer to the Virtex-5 GTP RocketIO User's Guide, ug196:
If the application under test would benefit from different settings for each tile in the GTP_DUAL under test, please refer to (Xilinx Answer 30947) for additional information.