I'm tempted to suggest digital noise particularly as it appears in the dark areas but I'd expect noise to show up in all scans not just those from Fuji negs since it can only be introduced by the scanner. Random thought only, you mention "boosting" in LR - could you also be overdoing the curves/levels in the scanning software for the Fuji frames? This can cause noise in the shadows big time particularly if a bit of neg underexposure exists.
Years ago in my early digital days I used to regularly scan 35mm colour negs of weddings and found that I got the best results by scanning without any curves/levels adjustments in the scanner, preferring to do all that work in Photoshop. Noise was often a problem particularly with dark suits on a neg that was a bit underdone and trying to do any sort of colour/density correction during scanning just made it worse. I think a lot of people would hold the view that the best scan is often one that looks a bit flat because it can be worked on later using better software. OzJohn