Hello!
I don't think it is any idea to start looking at graph/plot settings in this case, what you should concentrate on is the GPIB programming, since this is most likely the cause of your problems. I cannot give you any more tips and hints since I don't have the instrument you specified and I don't know how your program looks like. I might be able to help you more if you attach the program you are using.
Regards,
Jimmie A.
Applications Engineer, National Instruments
Regards,
Jimmie Adolph
Systems Engineering Manager, National Instruments Northern European Region