In simulation, the Transmit pins from one MGT are skewed by 32 UI relative to another MGT. This indicates a discrepancy in transmit path latency between two transceivers.
This issue is fixed in the 8.2.01i SmartModel. A patch is available for 8.1 tools. See (Xilinx Answer 23472).
The new model will ensure that all transmitters will have a deterministic latency, and because of this there is no transmit channel skew for channel bonded applications.
It is important to remember that in silicon, transmitter latency will depend on latency mode.
For more information on latency, refer to the Virtex-4 RocketIO User Guide.