5th gear makes noise in all the 6 speeds. I thought they made it better on the newer touring bike with the use of the IDS, but it's not goin' away. there's almost 20,000 members on here and I haven't read one post about somebody loosing 5th gear yet.
I have an 07 Softail Standard, and when I first got it I thought it sounded funny. I now use Spectro 6 Speed in the Tranny and Redline in the Primary. (Next Oil Change I'm gonna give the Spectro Heavy duty Primary Chain Case a try in the primary.) I've got about 22,000 miles on the bike and now I really have to listen to hear the 5th gear noise, and if I'm not listening, I don't notice it at all. Maybe I've gotten used to it or maybe it's gotten quieter, either way I haven't had any problems with it.
With all that said, in 1999 I bought a Honda Shadow and I thought the Tranny sounded funny on that. I worried about it for a while then I just got used to it. today that bike has 75,000 miles on it and has never had a Tranny problem.
My point is Motors make noise, Transmissions make noise, and anything that moves and has friction is gonna make noise. Get to know the sound of your bike, that way when something goes wrong you'll know it.