Solution
This behavior is expected because FlexLogger handles manual stop events separately for each device. Since the PXIe‑4300 and PXIe‑4331 run in different acquisition tasks, FlexLogger reads their data in 100 ms chunks. At a 1 kHz sampling rate, each chunk equals 100 samples. When you press the Stop button, FlexLogger logs whatever data each task has already read at that moment. If one device has just finished a 100 ms block while the other is still mid‑block, the final sample counts won’t match.
This isn’t a sync issue, it's simply the timing of the manual stop. If you want both modules to have the same number of samples, you should go to the Logging Specification >> Logging Trigger >> select Stop logging at channel rate when Test time elapsed.
For example, when you configure a test duration of 10.33 seconds at 1 kHz sampling rate, both channels end up with exactly 10,330 data points because FlexLogger holds the stop event until all channels have data past that timestamp and logs everything up to that point.
