Unable to acquire all the points in LabView screen

Hi All,
I am using Agilent 54642A Oscilloscope to acquire a waveform to be displayed in the output screen of a LavView program. But the Oscilloscope has the maximum no. of points capacity as 2000(From the manual described in the command WAVOIN. So if I give 2000 points as my input I get the output graph in a second but miss most of my positive peaks (As shown in the attached file). Anf if I give suppose 5000 points, the oscilloscope loads the Factory setting (Not the setting, ex trigger level, time period etc. which I have given at the input) and gives the correct graph but takes a lot of time to load.
Can anyone tell me, either how to increase the no. of points or what are the specifications of the factory set up so that I can incorporate those in the program and get some good result.  Please have a look at the attached files, RECO0008 shows the wave of the Osclliscope and RECO0007 shows the output graph of the Lav View program. Kindly note that the positive peaks are missing in the second file.
Thanks in advance,
Neelesh.
Attachments:
RECO0008.JPG ‏252 KB
RECO0007.JPG ‏293 KB

Hi,
I have check the access details everything is Ok. Would like to know do they have any  issues with "User defined dimension".
Regards

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