When using IBERT for Virtex-6, there is an option to use TXOUTCLK for the IBERT System Clock. When you use this option, changing the line rate of a channel in the ChipScope Analyzer effects the accuracy of BER calculations.
How do I work around this issue?
TXOUTCLK is the "reference clock" against which the line rates and clock frequencies are calculated. If the line rate of that channel is changed, the TXOUTCLK frequency changes, which effects all the other calculations in the Analyzer.
To work around this issue, do not change the line rate for that channel or generate multiple bitstreams with the different line rates you want. This issue will be resolved in ChipScope Pro IBERT 11.4.