So the bottom loop is running slower than the top. You can use a notifier to let the top loop know when to generate signals and when to skip it. Look at Notifier examples. Send a notification from the bottom loop after the DAQ has finished. In the top loop, use the notification wired to a case structure. If True, generate the signal and enque the result. If false, do nothing.
An alternative to notifiers is to play with the delay time. Increase the top loop delay until the two loops run more in sync.
