I've always thought it sounded Southern too. He seems to turn it on and off though. A really good example is in KTF An Evening With...~ I can hear it now in my mind. Right before they do the last song (KTF) he's talking about the new album and Tico's maracas. Then he goes into the "Southern accent" mode when he's like "And in case i forgot to say it, if I don't see ya again thanx for coming, we'll see you out on the road.." it is VERY noticeable.

I remember Howard Stern and Robin Quivers used to often make fun of Jon's Southern accent that he only has on stage..