Why have I never noticed this before? I accidentally heard my cat's heartbeat, and realised it was in pairs. So I thought, do you count all of them singly, or the number of pairs? Wikipedia suggests it's pairs, judging by the 72bpm heart rate sound on this page which is actually 144bpm:
Maybe when you take a pulse you only feel one of each pair (not that I've ever been able to find my or anyone else's pulse, I've always listened with my ear).