I have a 2006 FZ6 and have had problems with the steering bearings since I bought it in 06. They have come loose several times and this morning I had to repack them. The lower one was rusted badly. I repacked them for now but need to replace the lower soon. Thanks for the input on the AllBalls...I will use those instead of stock.
Bottom line is that moisture is getting past the bottom seal and entering the bottom bearing. I suspect this is an aerodynamic issue....bear with me.
I believe the front end design, particularly the faring, causes air to be directed right at the lower headset seal, pushing water up into it when riding in the rain. Here is why I tend to think this is true: shortly after the first time I tightened the headset, I took the bike up to 100 mph plus, at which time a bunch of rusty water and grease blew up between the fork and gas tank and all over my arm and shirt. This, I believe was due to the pressure within the steering tube housing in the frame increasing from air being pushed directly into it at high speeds. Air went in, pressure increased, grease (and water) came out. I cranked it up to high speeds again, and the same thing happened. The headset became loose soon after. I believe at lower speeds, water is caught up into that same air stream path and pushed past the seal...water being heavier gets past more easily. The seal wasn't designed to handle these types of forces...so I believe this is a Yamaha design problem. From what I've seen, the problem is not reported as frequently from owners of 07 FZ6s and up when the faring design changed...but I believe the fork, bearings and seals are basically the same.
Anyway, my $0.02 for what it's worth. It seems to make sense.