Just for the record, we got everything working.
Answer: The SERDES SER_RCOMP 1.4k resistor was left off (even though this is not used by the PHY).
The reference design has it, but we missed it.
Thanx for visiting the forum.
Glad you figured it out. In the future, such technical questions such as this might best be served by going through your field representative, who can if needed put you in touch with the support folks.