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I had a similar issue with the passenger side front window of my 08 Si sedan. When I spoke with Honda about it, he recomended a grease that is designed for the rubber parts of the car's trim (seal around sun roof, door seals etc). Its a clear silicone grease of some kind, the name of it escapes me, but had him apply some of the grease to the door seals and the noise went down some. Also they investigated the door window and found that the regulator needed replaced. Warranty covered replacement
Hope that helps
Ran
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