I have been reading here for a while but this noise post prompted me to become a registered user since my 90 model has this same noise. So far, all explanations given could have been the possible cause, but let me add a couple more. First, if your engine has a lot of time on it, the noise could be coming from the upper exhaust powervalve. If this is worn a bit, it may rattle with the larger exhaust pulses produced by the KX5. Another possibility for the noise also stems from the big motor's strong power pulses at idle. This has to do with the straight cut gears in the transmission. All modern motocross bikes have straight cut gears(as opposed to helical cut) for strength, but they can be slightly noisy. You dont hear this noise on smallbores, but you can hear it in the big motor because every time that piston fires, it is rocking those gears back and forth against each other. This second explanation is what I always believed the noise in my KX5 to be since the topend is new(I put it there in 1994

), and the powervalve assembly is in good order. The noise has always been there for the last 9 years and it always goes away if the rpm's are increased just slightly.
This was quite long for my first post, but just wanted to contribute a little.
Gary