I'm inclined to blame the OS. You didn't mention what the is, by the way. If it's a unix variant, you could try renicing the program to give it a higher priority. (There is also a way to do this under windows, but I don't know it off the top of my head). I don't know that it would completely solve the problem, but if it makes a difference in your test results, it would imply that your program is not getting enough CPU cycles to do this in real time.

One non-perl solution could be to use a microcontroller (eg arduino) to communicate with the device. It could handle the triggering and also report back to the PC when it has happened.