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my guess is that you are generating huge amount of data (as you said), and you are using the LVM express vi. each time it is called it opens the file, write data to it, then closes it. Once the file size becomes big enough, things will slow down, I have seen it and there has been several threads about it.
Instead of using the LVM vi , open the file first time you access it, then write data to it and do not close it. Next time you write data to it (it is already open, just write to it(appened option).
After data Acq is finished, write data for the last time, then close the file.
(look at a LV example of streaming data to disk.)