We routinely have any male cats in our litters, who are not going to be used in our breeding program, neutered at the age of 3 months. Having it done this early, it is before they begin spraying, since once they do, they will continue to. This is probably what happened to your male who wasn't neutered until he was a year old. It's also very possible that there is a person living nearby who thinks your male is 'their' cat, and is feeding him, and letting him in, while he's away from you that long.
If people would be more open to having their cats (and dogs) spayed or neutered, unless they will be intentionally bred, there would be far less precious little animals used in medical testing, or humanely (hopefully) put 'down' by animal control agencies.
Please remember that if you're looking for a kitten or puppy, to always check at your nearby shelter for one, unless you want a specific breed. If you know what breed you want, please do not buy from pet stores, but go to a reputable and responsible breeder. Honest, the prices can be much less from breeders who often are looking for good homes for the little ones (and sometimes adults). Believe me, we have a few purebred Burmese currently, that if I could find them a good home, I would *give* them to people. They won't be used for breeding, they're already trained and their personalities are developed, but they will (I've seen this) adopt a new owner willingly, and be just as affectionate as if they had been gotten when they were kittens.
BTW, all of our cats are strictly indoor cats, and will in fact, avoid open doors.