Timing issues with parallel while loops

[CFER_STS]

I also want to add:  Your data acquisition loop appears to contain some sort of file logging SubVI?  Are you just appending data to a file here?  If so, there is no reason to be opening, writing to, and closing a file on disk every half second.  Use a queue to buffer your data in the main loop, and batch process that data at a much slower rate to log to disk.

[CFER_STS]

On the subject of timing and synchronization, I presume that you have other code which is accessing the Numeric 2 and Numeric 3 counter indicators at extremely high rates?  Otherwise, there isn't much point in attempting to increment those counters at 100 nanosecond resolution, while your main loop is sampling those values at 50 millisecond resolution.