Greetings,
I just had the chance to read over this discussion and had some suggestions for your application, as well as comments on posts by other users. First off, I believe you are using the PCI-5102, which is one of our digitizer boards. As you probably know, the digitizer has nothing to do with digital inputs, as was implied by markwysong's comment. This is simply a high-speed DAQ board.
This board supports analog and digital triggers. Since your square wave pulse is not constant, I would just use triggers to detect the pulse. You may want to look into "retriggering" or the ability to trigger once and then configure the trigger again. This is because you know you are going to receive a 10ms pulse, but you don't know when and it will not happen
at any specific frequency. So, you could either connect the pulse to a digital line and poll it, as you are doing now, or just connect the pulse to a digital trigger line.
Regards,
Justin Britten
Applications Engineer
National Instruments