Are you using any mods ???
The way you use mods is to get the JSME utility (JoneSoft Mod Enabler) and you can add and/or subtract mods without messing up the original files. This way you can try different mods to see if it will over ride the offending file that is causing your noise problem.
You can get his mod by going to the Subsim SH3 download site or over at U-boot.realsim.com site.
http://u-boot.realsimulation.com/ or go to the SH3 Workshop site and look under the sticky where the mods are located and you can download it there too.