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Hello Jason,
You are correct that the CompactDAQ chassis has an onboard analog input sample clock.  We can see of page 66 of the NI cDAQ-9172 User Guide and Specifications that the timing accuracy of this clock is 50 ppm of the sample rate that you specify.  Since timestamps are calculated directly from the sample rate in your program, the accuracy of the sample clock will determine the accuracy of the timestamps relative to each other.  If you are acquiring data at 1000 Hz, the accuracy of the sample clock will be ± 1000 Hz * 50 ppm or ± 0.05 Hz.  You can also view this as a sample period accuracy of ± 1 ms * 50 ppm or ± 0.00005 ms.  I hope this helps!
Best regards,