We should make sure that your computer is picking up the signals from each of your boxes at only the intended port. Oepn the IO Test application (if you used the default settings when installing DirectRT, it should be located at C:\DirectRT\Utilities\TTL. The folder also has a readme file with instructions).
Make sure that the IO Test is only showing results for one button box through the port assigned to it and nothing from the other box. This way we can limit the problem to the hardware or whether it is something with the software.
Also, exactly what kind of button boxes are you using? Did you purchase them from Empirisoft? Just curious.
Jason Reed
Empirisoft Software Support Specialist