Hi Kevin,
You can achieve throughput rates an order of magnitude faster if you use the DMA FIFO transfer method versus front panel arrays. You will also have the benefit of DMA FIFOs taking up *significantly* less space on the FPGA than front panel arrays. Depending on what else your application is doing, you may be able to still do everything you need to through the front panel data transfer, but I highly recommend using the FIFO instead. If you're worried about data loss, just monitor the Full? output of the FIFO Write function on the FPGA to determine if any data is being lost.
FYI, we have a separate board for cRIO questions - this board is meant for the LabVIEW Embedded Development and LabVIEW Embedded For Blackfin Processors modules.
Cheers,
Matt Pollock
National Instruments