There are people fortunate enough to live in a good location where simulcast interference is minimized. If the system you are listening to is simulcast, you did not load the nearest tower only. You probably loaded the nearest site. In a simulcast system, a site is not a single tower but rather a collection of towers all transmitting on the same frequencies. The scanner and the scanner software cannot distinguish between between one tower in a site and the rest of the towers in the site. But if you are in a good location relative to the towers, you may not be affected by simulcast that much.I'm not sure if I'm missing something but using Free Scan, I programmed my 996P2 for the Cobb County simulcast system but only loaded the tower nearest me into the radio. No issues what so ever, in fact it sounds better than my department mobile XTL5000.
In some cases, people think they aren't having simulcast issues until they later realize they are missing transmissions. But if you have a commercial radio that you've used for comparison, that's probably not the case for you.