Hello,
1) I would suggest trying the example that ships with LabVIEW Real-Time called One Channel PID - RT Engine.vi. The VI you are using sounds like it is doing buffered AI-AO. Your application sounds like it would be a single-point input, followed by single point output. If you are doing more than one channel, you can look at some of the multiple channel PID examples. The point here is that you use single-point input (one sample from each channel of interest is acquired per iteration) instead of buffered input, and that you can remove the PID portion if you are not interested in PID control.
2) Try a single-point example as mentioned above. Do you see the same behavior? I have never seen this happen and do not know what would cause this offhand.
3) Ye
s. It is generally recommended to only have one time-critical VI though, and not to run parallel DAQ VIs.