Hi alexndr,
You can use either the Reset or Abort method, depending on the behavior you want. Reset will abort the FPGA VI and then reset it to its default state. Abort will not reset the default values, which should be considered if the VI is going to be run again. An alternative is to use a control to
stop the VI.
Another difference between Reset and Abort, as you have seen, is the output state of the CompactRIO channels. This is discussed in the LabVIEW Help topic "Understanding Power-On and Start-Up Output States for CompactRIO Output Modules." It sounds like the VI is set to load on a reset, which sets the output channels to their start-up output states. Using RIO Device Setup (Start » Programs » National Instruments » NI-RIO » RIO Device Setup) you can configure whether a VI is loaded on a device reset. You can change the start-up state through an FPGA I/O Node in the FPGA VI. With the Abort method the channels return to their power-on states. For the 9401, the line direction defaults to "Input" when the device is initially powered.
Hopefully this helps explain the behavior you have seen.
Jennifer R.
National Instruments
Applications Engineer