Why are there gaps in my waveform graph after peer-to-peer streaming?

I am generating an arbitrary waveform with the PXI-5412 Arbitrary Waveform Generator and reading them with a PXIe-5122 Oscilloscope. I am then streaming the waveform to a PXIe-7846R FPGA module with Peer-to-Peer Streaming and sending the waveform back to the Host through a DMA FIFO. However, when I graph it, there seem to be gaps in the waveform. Any idea what would cause this? I have attached a screenshot of one graph when reading directly from the waveform generator, and one when passing the waveform to and back from the FPGA where the gaps appear.