Whenever a PCI-650x board is configured for output, its digital lines will always reset to logic low. The glitch that is seen is around a 5 ms dip low from the time of the configuration until the software gives an output signal.
The workaround is to set the jumper on your board which configures the power-up (input) state of the lines. You can set the power-up state of the lines to low, and then there will not be a dip after configuration. If this power-up state is not satisfactory, then an inverter can be used on the output to switch the logic of the lines.
The Developer Zone article linked below contains additional information on this topic, including information on the 653x boards which do not reset to logic low when configured for output.
What Is the State of My Board's DIO Lines When My Computer First Turns On?Sonya Wornson
Applications Engineer
National Instruments