My Dad and I both have 06 LE model Hayabusas and both of our bikes had the knock. Dad's bike knocked a lot harder than mine and after fighting with Suzuki for 5 months they finally agreed to look at it. Suzuki installed the wrong main bearings. When the mechanic took his bike apart he called the regional manager who walked him through the fix. Basically, the bearings in my Dad's bike were identified as "Yellow" and the bearings he needed were identified as "Purple". I cannot tell you the difference between the two. My bike never went in, still knocks, but runs super hard. I was given the "if anything happens we will fix yours too" statement in writing so I am not overly worried about it. Dad's bike does run quite a bit better than mine though....meaning smoother with slightly better accelleration. Oh, and he is getting between 46 and 50 mpg w/regular riding and around 36 to 39 mpg w/aggressive riding while I have never seen over 42 mpg.
It is my understanding that there were a run of 06 LE's that had the wrong size bearing installed and that Suzuki knows about it. I can tell you this much, when I was calling in initially Suzuki had 4 other 06 LE's on the books with the warranty repair and 4 more calling trying to get the repair. All of this took place between January and June of 07.