1. Give us a link to what you read in the forums about the limitations in the determinism of the 1 MHz clock so we can read it too. Why do you think the Windows OS would give you problems with the real-time OS on the target? What is the target? What code are you running in Windows and what code are you running on the real-time target? Where is your control loop running? Something doesn't sound like it would work right if you are trying to use a 1 kHz loop to control a 1 kHz vibration. I think you'd need to run at least twice as fast (based on Nyquist) to have a chance, and probably at least 10 times as fast.
2. If you feel you are losing data points in your acquisition, post your VI's so we can see how you have them set up.
