Could you please post your VI so that we can get a better idea of what you are doing?
Because the DAQPad-6507 is a 8255 based device, the digital lines on ALL of the ports are reset when you change the configuration one digital port. This may be the cause of the undesired behavior in your VI. For more information on this, read the link below.
Why Do All My Digital I/O Ports Reset When I Configure One Port?
You should not use multiple Write To Digital Port VIs when writing to more than one port. Instead, you should call each DIO Port Config function (one for each port) all at the beginning, and then call your DIO Port Write functions. I have attached a screenshot of what this should look like for your program.
Hope this helps!