If you are using DAQ_Rate to calculate your sample interval and your scan interval, you are more than likely going to request an unsupported timebase on both of your E-Series boards. Since you mention that the timebase for both boards is 1 MHz, this is most definitely occurring. DAQ_Rate has no way of knowing what kind of device that it is calculating these parameters for, and thus it will return whatever parameters make the most sense according to its algorithm. For example, E-Series boards only have two possible timebases--100 kHz and 20 MHz, but DAQ_Rate suggested 1 MHz. Unfortunately, you have no way of knowing what SCAN_Start coerces these values to. You are much better off calculating the sample and scan parameters manually and passing them directly to SCAN_S
This issue may be the source of your problem.