The answer to your question depends on which DIO96 board you have.
When the computer is first powered on, all lines on the board are configured for input. Internal "pullup" or "pulldown" resistors determine the logic state of the input line. If a pullup resistor is present, it connects the line to +Vcc (+5VDC); if a pulldown resistor is present, it connects the line to digital ground.
The PC-DIO-96 and PCI-DIO-96 resistors are 100k pull-up resistors and can NOT be set to pull-down.
The PC-DIO-96 PnP resistors are pulled up or down through a 100k resistor which can be selected by switching jumper W1.