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PXI-5122 digitizer, triggered dual waveform acquisition

Hello, again, NI world. I have a question about how the PXI-5122 acquires triggered waveforms in relation to one another. I am acquiring a logic waveform (from whose falling edge I am triggering my acquisition) along with an out-of-sync (and therefore rolling on the display) sinewave that drops to 0 every 5.7 cycles. My test is to verify that the negative pulses on the logic waveform coincide only with positive peaks on the sine waveform. Due to the out-of-sync issue, it can be very difficult to see, so we have a feature on our scope display that allows us to stop acquisition, in effect, to pause. Sometimes the pause shows a perfect alignment, other times, not. So...my question is:  When acquiring 2 channels of data, triggering off one, are both channels acquired simultaneously (is the data interleaved or saved to buffers in a parallel fashion?) or is one channel acquired in full, then the other? Can find no source that tells me how this is done.

I am attaching (I hope) a pic showing a bad alignment. A good alignment would show the wide negative pulse on the logic waveform aligned with the wide zero area on the sine waveform; then the narrow negative pulses align with positive peaks on the sine.

Thanks for any insights.

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