The usual reason this happens is because the Easy DIO VIs reconfigure your board each time they run unless you wire in the iteration terminal. Reconfiguring your board resets lines. Even if you do wire in the iteration terminal, the first time an Easy DIO VI runs it configures the whole port as input or output - clearing your previous port configuration. If you are using traditional DAQ, the best thing to do is use three advanced VIs: DIO Port Config.vi, DIO Port Read.vi, and DIO Port Write.vi. You can find these on the advanced palette or on the diagram of the Easy DIO VIs. Call DIO Port config.vi only once and configure your individual lines as input or output (assuming your board supports individual line configuration).
Regards,
Doug Norman