I think TD's right about the saddle. But do check all the screws holding the bridge down. Anything that is not tightened down will rattle. I once thought that my bass had a rattle in the low E...which turned out to the the snare on my son's drum kit that was rattling.
Couple of things to keep in mind: Always do your buzz tests with ALL strings at at tension and in tune.
Can tuners buzz? Absolutely! I was having a terrible time getting the buzz out of my acoustic, until Simon Barden on this forum recommended that I tighten the tuner nuts. Voila! (as my Quebecois grandmother used to say). Almost all of the buzz went away. Under tension the geared part should be quiet and the post should not move. If the post will wiggle under tension that could be a problem. I'd recommend tightening anything that can be tightened. I use a "three finger" rule. Tighten everything until it stops using my thumb and two fingers on the screwdriver. EVERYTHING on the tuner: knob, bottom screws, and top nut.
screw down everything that can be screwed down everywhere on the guitar including the pickguard and pickups if they are on.
Eyeball the neck from the heel looking up the fretboard to see if there is a twist. If not...
Redo the fret leveling with a longer stick. I don't think this is the issue, but it's worth a try.
Use a fresh set of strings. They don't have to be good, just "intact".
Redo the first three steps in TRAIN:
Tune
Relief (get it flat then reset the truss rod--with capo on fret 1)
Action (set the action at the bridge--with capo on fret 1)
If you still have a buzz at that point we may need to get out the auto mechanic's stethoscope to figure out where it's coming from!
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