Hi,
Are you using labVIEW or C?. Also, are you using the traditional or IVI driver?.
I looked at the traditional driver for labVIEW and it comes with an example program to acquire a a 2500 point waveform. You can use NI-Spy to capture the commands issued to the instrument and compare it with your application. Also check the user manual for inforamtion.
Hope this helps.
DiegoF