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simulation loop timing

I am having trouble runnnig my simulation in real time.  I am using LabVIEW version 10.0F2 and acquiring signals using a PCI-6230. In the simulation loop parameters, I am using the solver: Runga-Kutta 1 (Euler) with a step size of 0.005, and in the timing parameters I have it syncronized with the timing source, source type: 1 KHz clock with a period of 5.For a relatively simple VI these settings seem to work just fine. In a slightly more complicated VI, which happens to be saved as a Simulation SubVI for another VI, I see that the loop timing is completely off. Also by removing components of the subvi the timing changes drastically. Please advise.

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