phase problem about transceiver of stratix ii GX

I retract my previous statement. I did not pay close enough attention. You are saying that the individual bits of the serial output are not phase aligned. Is that correct? If so, the behavior is likely caused by the serializer itself.

The only way I can think of to remove the skew is to operate the transmitters in bonded mode. Bonded mode is intended to specifically remove that channel-to-channel TX skew. However this imposes certain restrictions which you may not be able to live with in your design.

What mode are you currently operating the transceiver in? Are all of your channels located within the same Quad?

Jake