Just a heads up - you may find this thread gets "moderated", because discussion about almost all scanning issues is prohibited on APUG.

That being said, there is a very good chance that the problem is with the scanning, because scanning software adds so many variables to the equation, and because it is extremely difficult to get scanning software to give you a truly "no corrections" file.

The fact that you are happy with the scans from transparency films just tells you that your scanner and software happen to be well set up for transparency film - not black and white negative film.

Show us a photo of your negatives, and we will be able to tell you more.