When a ChipScope IBERT Core is generated, certain attribute settings are included in the UCF file to start up the core at the line rate specified by the user. If the exact same parameters are used in the RocketIO Wizard (line rate, refclk rate, fabric width, etc.) for Virtex-4 MGTs, slightly different attribute settings will result.
Starting in 9.2i ChipScope, the settings will agree between the ChipScope CORE Generator and the RocketIO Wizard. However, if the line rate is changed at runtime in the ChipScope Analyzer, there might be some small differences between the new line settings and the settings generated for that line rate in the RocketIO Wizard.