Is the console out switch on the cRIO off? Make sure the cRIO isn't imaged with the serial CAN plugin.
What serial levels does the arduino serial port use? Many microcontrollers use TTL levels, which violate the RS-232 spec. You'd need a level converter like the
MAX232 to use it with the cRIO.
If you post the gibberish and an example of what the GPS sends, someone might be to make sense of it.