Hello,
I am not sure where the problem lies in your application, but here is one test you can run to see if the card is working correctly and it may be something that we are missing in the programming of the card.
You can open the Pattern Input example and the Pattern Output example VIs in labview.
Next, tie all the data lines of port 0,1 to the data lines of port 2,3. Also tie REQ1 to REQ2 (clock line). Then you can start one example with the settings of external clock, then start the other program using the internal clock. This will insure that we start the slave ports first, then the master ports will start the transfer of data after the slave ports are ready.
Hope fully you do not see the same behavior, but if you do, you may wish to contact NI technical
support. For contact information visit www.ni.com.