Hi Julia,
As I understand it, you observe some problems when trying to perform a link BER test between CV TTK and A10 TTK. Based on your description, one of the possible reasons might be the patterns between the CV TTK is not directly compatible with the A10 TTK. Sorry as I do not have the visibility into data transmitted from the TTKs but this is just a suspect.
As a workaround, you may create simple test design with PRBS generator and checker. Run the BER test and monitor using signaltap. You may in parallel use the TTKs to dynamically tune analog settings on both device and monitor the BER in signaltap.
Please let me know if there is any concern. Thank you.