This Answer Record describes digital simulation (Smart Model) issues that are important additions to the information listed in Chapter 7 of the Virtex-4 RocketIO User Guide:
The period of the incoming RXP/RXN signal must be restricted to an even number of picoseconds. Because of the way the Smart Model accounts for PMA operation, incoming signals with an odd period (e.g., 321 ps) will result in loss of lock.
This restriction also applies to the MGT reference clock. This clock should be rounded to the nearest 1/10 of a nS. For example, use 4.2 nS instead of 4.17 nS.