Basically I'm using LabVIEW 2011, NI cRIO-9118 Chassis, NI cRIO-9014 Real-Time Controller, one NI-9205 module (for Displacement), three NI-9239 modules (for Acceleration), three NI-9236 modules (for Strain Gages), and one NI-9401 module (TTL for indicators).
I used flat sequence (just like the examples that I saw in the help) for the FPGA VI with three while loops in one of the sequence. The first while loop is for the acceleration (NI-9239) with 13 channels for FIFO(1), the second while loop is for the displacement (NI-9205) with 12 channels for FIFO(2), and the third while loop is for the strain gages (NI-9236) with 25 channels for FIFO(3). All the while loops are inside one sequence.
Same as the examples, I used while loops for each FIFO for the Host VI. I have a total of four while loops in the Host VI, one for the commands and three for each FIFOs (1, 2 and 3). The programs runs and collects data but when you see the elements remaining for each FIFOs, it spits a large number meaning it might be losing packets of data for each FIFOs. I have use LabVIEW 8.5 and 9.0, but I never got any large numbers coming out of that indicator (FIFO elements remaining). What is causing it to spit our large numbers of FIFO Elements Remaining? Also in LabVIEW 8.5 and 9.0, I can go each FIFO properties (from the project tree) and select the DMA Channel (1, 2 and 3) for each FIFO. Meaning I can select DMA Channel 1 for FIFO 1, DMA Channel 2 for FIFO2, and DMA Channel 3 for FIFO3. LabVIEW 2011 doesn't give you that option so I'm not sure if it's automatically selecting the right DMA Channel respectively for each FIFOs.