I'm pretty sure your problem is that your sampling your first channel before the output from your AO channel has updated and settled. See the attached picture for a better look at the timing signals. By default, the first AI channel conversion will take place 100 ns after the sample clock. However, for the 6221, the slew rate of the DAC is 15V/us. Depending on the step sizes of your output waveform and the desired settling time, you will have to push the first conversion out further from the start of the sample clock if you want all channels to sample the same data. I'm not sure which API you're using, but in LabVIEW you can tweak this by using the More->Delay From Sample Clock->Delay and Delay Units properties in the Timing Property Node. In the other text based ADE's, you should find similarly named get/set function names (e.g. DAQmxSetDelayFromSampClkDelay).