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I am not at all sure what the source of your problem is. An NaN would results because of erroneous data being read from the buffer. Be sure that your buffer is big enough, and that you are reading it often enough. Look at the examples for information on how to do circular buffering.
High Speed DAQ is a touchy subject. You have to be VERY careful about your configuration. There are delays, timing, and other setting issues that must ALL be taken care of in such applications. I once ran into a problem where I actually had to modify the interchannel delay because my scan speed was high, and my gating setup was such as to cause issues. It is not entirely well documented as to how to set these things (at least not in the VIs themselves.) Be sure to r
ead through your DAQ manual. It also helps to create a timing diagram. Be sure to include any hardware related timing data in your diagram, such as interchannel delays, gate widths (from your channel and scan clocks) etc. Not only will this help you solve your problem, but it will help you gain a much clearer understanding of the limitations of DAQ.
Good luck