I'm at almost 40,000 miles on my '99 and I just installed the FOURTH set of seals! The bike had a leaky seal when I bought it in '01 with ~3600 miles on it. I've had to replace them 3 additional times. I like to ride hard and am VERY fat (~335 lbs nekid). I don't loft the front wheel - not because I am a good citizen but because I don't know how and am too chicken shit and afraid of wadding my pride and joy. I've had the seals replaced by GP Suspension in Oregon each time. The last two times I also replaced the dust wipers - the visible seal you see on the fork lower. After blowing the second set I had GP order a set of wipers - the thought being that perhaps they had 'aged' and lost their elasticity and so dirt/grime/bug-guts was getting past directly to the seal itself. Sure enough the new set mic'd ~1 mm smaller inner diameter than the old set. Anyway, I got ~18,000 miles on the last set of seals with new wipers which is a big improvement over what I was getting with just seals alone. I had them install new wipers again this last time figuring it's cheap insurance. FWIW, GP Suspension is a well known and respected shop that primarily deals with race bikes (not only in the NW but Laguna, Southern Cal, Daytona, etc.). They check the tubes for straightness, etc. I don't know why I haven't heard more about 'busa seals blowing out or leaking. There does not appear to be anything wrong with my forks. I've added 1KG springs (to attempt to cope with my weight) and I don't believe I am bottoming the fork out at any time. Who knows. GP says they have seen a number of both 'busa and TLR1000 (same forks) with blown seals. Apparently the dust wiper design does not incorporate a tension spring to maintain tension on the wiper to prevent debris from getting to the seal. GP says that with Showa forks they can retro-fit a different wiper with the tensioning spring but one does not exist for the KYB fork ('busa).
Anyway, probably not what you wanted to hear. It costs me close to $300 to get the seals replaced (includes complete overhaul) and now that I live in Montana I have the addition of shipping charges. I guess the bright side is that I get fresh forks on a regular basis.
Try keeping the fork tubes clean at all times. One of the times I lost a seal was right after a 4000 mile road trip. I had gone through Yellow Stone and hit a thunder storm. The road grit dries like cement and I believe I may have got some on my forks and not washed/cleaned them well the next morning at the hotel - I mean I like my bike to look good but on a long trip where it's going to get filthy everyday I figure why spend an hour every morning cleaning it. A quick once-over with S100 or Honda spray polish and it looks great. Now, I try to wipe the fork tubes down whenver I can remember.
OM Gang