I've neither the time nor inclination to further look into it but if you play around with flightaware it actually shows two flights: SJU-PHL (op B767) and the next PHL-MAD (op A333). I can't be sure but it they do look totally unconnected to each other; there is a two hour gap between the 767 arrive in PHL and the A333 leaving.
I'm not 100% au-fait with the American way of doing things, but this seems to me pretty ridiculous. Why why why are two separate flights operating on the same flight number? There are enough numbers out there to give each flight their own right? What if the SJU-PHL is delayed by more than 2 hours, is the MAD flight allowed to go? If it does will it melt the computers (and ops staffs' brains), by the simple fact there are two US740s airborne?
You wouldn't catch BA for example operating BA123 MAD-LHR and then a couple of hours later BA123 LHR-JFK on a totally different aircraft... there's no reason to do it...
I realise that these are relatively minor issues, but why bother with the fuss?!