Greetings,
Well, it seems quite odd that the board's outputs would be inverted. Let's open the Measurement & Automation Explorer (MAX) utility and run the Test Panel on your PCI-1200. In the Test Panel window, go to the Digital I/O tab and set your DIO lines to be output and set them all high by clicking the check box and making the LED red. Now, go ahead and measure your DO lines and see if the voltage is 5V or a low voltage. You should first disconnected all external circuitry that may be connected to your output lines.
Let me know if you measure a voltage other than logic high.
Regards,
Justin Britten
Applications Engineer
National Instruments