what kind of switch integration are you working with here? did this just recently start doing this or are you installing this 2.4.6 system new?
sounds like the call coming into port 1 is being reported to us as a direct call instead of a forwarded call - pop open the call viewer application (you'll find it under the tech tools directory in 2.x land I believe, although it's been a while since I've poked around on 2.x). It'll show what is being reported to us from the switch here.
If you call in from the user's phone directly to voice mail does that work? Be sure to try it with port 1 busy so it forces a forward to port 2 or greater when trying this...