Hey lihui,
Based on what you have posted, you can probably guarantee that the GPIB card is working properly, because it is communicating with the other instrument. The next thing I would try is to change the GPIB cables. In some instances a bad cable can prevent data from transmitting on specific lines and they can be intermittent. When you connect the cables make sure you tighten the screws on the cables to ensure a good connection.
The next thing I would suggest is using a GPIB analyzer to look at the bus lines to see if you can see any difference between the responses of the two instruments. This would let you know if one line was not working or perhaps the hand shaking was having problems.
I hope this helps out.
JoshuaP
National Instruments