Ya know, I have often had that issue when pressing record for a punch in with mouse. I have a Steinberg TP controller that I use that always nails it. Not sure what causes this but it is friggen annoying.
Not sure this is related, but I can't count the number of times I felt stupid because I got mouse happy and forgot to use the damn controller and a punch didn't happen. Sometimes hitting record button just doesn't work with the mouse.
I have no idea what causes that in my situation and not sure it helps you at all....