If you might be paused long enough for the DAQ hardware to overrun the buffer size, you won't be able to use the (-1) option to read "all available samples" anymore. Your Read call should be returning an error when you make an attempt to do this -- are you handling it?
It sounds like what you really care about is more like "most recent samples" and there's a way to get those directly. Under LV, there's a DAQmx Read property node where you can set "RelativeTo" = "Most Recent Sample" and "Offset" = -N, and then request N samples.
-Kevin P.
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