Curious, I don't remember seeing this. Could it be you are inadvertently "hammering" the CPU?
What is the VI priority setting? (If you e.g. force time-critical, unimportant things will get delayed). Leave it at "normal". Is you code clean, with proper waits inserted or is it just spinning <b>all</b> loops as fast as it can? What else is running on that PC? Is it communicating with DAQ hardware?
