Scaling is application controlled. It has to be willing to use a larger window size.
SSH and FTP do not pick up and use larger windows by default. HPN-SSH specifically addresses this problem. Some implementations like Solaris can pick up larger sizes as well, but the APP has to decide to do it.
Larger TCP Window sizes are slowly creeping into applications, but by no means standard.
I have been fighting this specific issue in my job for the last 4 years, constantly seeing NFS/CIFS/FTP/SCP and lots of other applications like DBs, plus data migration tools like DoubleTake, Platespin, and TDMF trying to pull data over LFNs and using less than 10Mbits of an OC-3 to OC-48 that is no where near capacity or even totally silent.