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First off I would like to welcome you to the NI forums and thank you for posting your issue.
I have been playing with a USB-6509 and the program that you posted. If I understand the issue that you are having correctly you have tried to connect Port 0 to Port 1 where Port 0 is your Digital Output and Port 1 is your Digital Input and when you try to use the program that you attached the digital output that you are trying to read will clear the digital input port that you are trying to write to. Is this correct? I was able to connect Port 0 to Port 1 and use Port 0 as an ouput and then read the data from Port 1 using your program.
I want to make sure I am understanding the problem correctly.
I struggled a little with the port settings of USB-6509, but I was able to set single ports as outputs or inputs (not single lines, as I tried in the beginning). In particular I use the following:
P0, P9 and P11 out
P1, P2, P5 in.
I attach the task definition file for it.