I also experience this effect with scanning Colour neg film, not B+W nor E6. My solution is relatively cheap and effective. Neat Image software works a treat, also Noise Ninja although that was dearer - hence my choice. It will work wonders with B+W if you want grain free HP5 for instance.
Plenty of sliders to twiddle with, personally I have found that Auto works very well indeed. Worth saving profiles, dependant upon neg size,/resolution etc. CAn then reuse these, it gives assessment of matching before carrying out the noise reduction.