Hello;
You didn't mention how you are synchronizing both device, however, the best way to implement a syncrhonized data acquisition in between multiple devices is by the use of the RTSI bus.
You can connect both devices through a RTSI cable, and share the same AI Start Scan clock to clock both analog input tasks.
You also didn't mention what programming language you are using to program the devices, but there are examples on how to synchronize multiple devices both in Labview and NI-DAQ functions.
Hope this helps.
Filipe A.
Applications Engineer
National Instruments