That sounds really strange, I didn't think the NI-CAN cards have the ability to go into listen mode (some other companies CAN cards are able to listen without acknowledging the message)
First, did you check the power jumpers? You can power each device internally or externally, which is selectable by a jumper on the board. (look at Appendix D & E of the NI-CAN User Manual)
Second, check the termination resistance, is it different for 1 port compared to the other, and is it correct? NI gives direction on how to replace the termination resistors of their cards. (look at Appendix D & E of the NI-CAN User Manual)
If you try these 2 and still get no change, I would call NI.