Hi Romain,
I understand that you are overwriting data in your buffer before the system has a chance to retrieve the data. Increasing the size of your buffer should alleviate this error. If you are using interrupts (IRQ) rather than dynamic memory accesses (DMA) to transfer data from acquisition to system buffers, you could also switch to using DMA since it is faster than IRQ. Note that some data acquisition devices only work with IRQ, not DMA.
Please let us know if these suggestions do not help resolve your issue.
Best regards,
Marcus G.
Applications Engineer
National Instruments