If you are using CVI, you could set in MAX your port as an input (or output) port and then programmatically set single line as output (or input) with the line
DIG_Line_Config (board, port, line, direction);
I made this in an application wih a PCI-6031E and it worked well. I suppose your card too is able to manage single lines of the port with different directions.
I saw that even with the port configured that way it was possible to read it as a complete port. I didn't looked at the value for bit that match the output lines: I suppose they are not relevant. But other bits are good.
Roberto