I am not familiar with the PXI-5600, but if you create a loop that just reads the 5600 and stores the data in a queue, it should run fast enough to keep up with any DAQ device, and should be able to take 1000 readings per second. If you use express vi's, that may slow things down. You may have to use lower level vi's. In a second parallel loop, read the queue to process the data. This should speed things up. Be sure to put some time delay (10mS) in each loop to allow the CPU to perform other functions.