Yes Jimjib, everything that Lyle said was true. First no matter how much electrical noise non-resistor plugs cause, they shouldn't be able to cause anything when they have no power. (your ignition switch was off!!)
On my bike I was having what seemed to be a fuel cutout. The problem was that when it cut out it wouldn't start anymore. The starter cranked but the fuel pump wasn't being energized. Anyway, I took it to the dealer who looked at it 6 days after I dropped it off. He told me my TPS was out of adjustment and that's why it wouldn't start. I thought to myself, this guy's an sugar! There is no way the TPS can affect the power going to the fuel pump relay. Well I picked it up and it ran so I figured he must know something I don't and off I rode, happy and unsuspecting. A week later, sputter, cough, sputter, the problem came back. Dead bike. Not starting again. Towed it to the dealer since I was stranded and he looked at it right then and there. He noticed that the wires leading to the right hand control pod were quite hot. He also noticed some wires under the seat were squished by the fuel pump relay bracket and pulled them out. Then the bike fired up. He also noticed my A-Tech fender eliminator kit and said since it was aftermarket they wouldn't do any warranty on my problem and I should find the short myself. Well I did just that since they seemed to want me out of there and I don't trust any dealer mechanics anymore.
I got home and took apart the wiring harness all through the back section of the bike and inspected each wire and coundn't find any type of cut or short anywhere. Now puzzled, I went back to the wires leading to the right hand control pod since they were the ones that got hot when the bike wouldn't start. I took off the wire covering sheath, which involved removing the connector plug on the end and lo and behold I found the short. I posted pictures on Labusas.org under "Here's my short".
This is what I found after examining the wiring harness of the Hayabusa in two separate places. In some places in the harness, Suzuki had to splice two wires into one or vice versa. Where these splices are, one of the wires insulation is stripped off and the second wire is connected to it with a small brass crimp connector. Then that is covered with one or two wraps of thin electrical tape. On my bike the sharp ends of the wire stuck out a little and cut through the tape and then cut into an adjacent wire causing an intermittent short. I have heard of some Hayabusas with wiring harness' being replaced and I believe that crimp connection is the reason. Since dealers don't or won't spend the time to track down a short they usually replace the harness or just give the customer a BULLSHITE explanation for their bike problems.
I'll bet money that is what is happening with your bike. Somewhere in your wiring there has to be a short circuit. I'm not sure how to tell you to fix it since I have some experience with electronics and love to work on my bike. I spent about 3 hours studying the wiring diagram and tracking down and fixing my short. I doubt your dealer will put that kind of time and TLC into it either.