The reason this happens is because of the VI's you are using. The Write Digital Line VI and the Read Digital Line VI both contain a VI in their diagram called DIO port config, which configures the entire port. These easy VI's configure the ENTIRE port for input or output. If you don't have the iteration terminal wired on either of the Write or Read Digital Line VIs, then the port is configured as output or input each time your loop runs. Therefore, when you read a line, any output that you were driving turns into an input, and the output at that line is lost.
The way to fix this is to modify the Write and Read Digital line VIs and save them as modifications, and changing the line direction map of the DIO Port Config VI. Therefore, you can map your port as indep
endent inputs and outputs, and not all as input or output. The help on DIO Port Config tells you what to input at that terminal to designate an input or output line.
That should fix the problem.
Mark