You have to remember that these ol' bikes do vibrate a lot. Like I mentioned earlier, my biggest rattle comes from the clutch lever. But I've had a few other rattles as well, like the headlight ears shearing off of the fork shrouds. That was a fun one.
But if everything is tight that you know to check, and it's not terribly loud, you are probably fine. I've had myself all geeked out over nothing before on my bike. Wear the full face helmet all winter and spring then summer comes and I put on the half helmet and I start freaking out "What the hell is that noise?!" 30 miles later "Oh, yeah, that's just my flat tappet lifters chattering away. Like normal."