Sorry, I misread your previous post. You are able to get the frequency you are looking for, but the amplitude of the wave isn't correct. We may just be running up against the system limitations of the update rate. We need the update rate to be a good deal higher (about 10 times or more) than the frequency of the wave for the waveform to have the correct shape.
I would like to check that your board is using DMA as the transfer mechanism, as opposed to interrupts. Your PCI-6025e only has one DMA channel, so if multiple operations are occurring, only one uses DMA and the others use interrupts. I am attaching the example you were using, modified to set the transfer mechanism to DMA.
Can you get a 100 Hz waveform 1 V peak to peak correctly? If you can, I think that at 1000 Hz, we are running into the system limitation and you may want to consider using an M Series device. The PCI-6221 has an update rate of 833 KHz and has 6 DMA channels.